Many areas of modern biology, from molecular genetics to neuroscience, are being revolutionized with new knowledge by analytical, computational and experimental research at the interface between physics and biology. Biological physics, medical physics and soft condensed matter physics are all interdisciplinary fields of physics. In these areas, scientists from diverse backgrounds explore the physics of single biomolecules, stem to nerve cells, organs to the whole systems, the application of physics to the needs of medicine, and the physics of biological materials. The Biological/Medical/Soft matter physics session of the ANPA conference to be held on July 14-16, 2023 will bring together basic, applied and clinical scientists working in these fields to share and discuss their recent research discoveries and methods. We welcome you and your colleagues to submit abstracts for oral and poster presentations, and look forward to seeing you at the conference.
Title: Resting state brain measures in healthy and patients population
Abstract:
The human brain is a complex organ, characterized with alterations/modifications, even too breakdowns, in the interaction patterns which are the hallmarks of diseased brains. In this talk, the speaker plans to introduce some of the resting state brain measures, network impairments and core cognitive deficits in schizophrenia, and comparison of these deficit patterns with the effects of drugs (ketamine and midazolam). In addition, cerebral blood flow and cardiovascular risk effects on resting brain regional homogeneity will be discussed. A brief summary of possible avenues for studying the human brain in health and disease will be provided.
University of Maryland School of Medicine, Baltimore, USA
Please look below for detailed schedule.
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Abstract Number: ANPA2023-N00027 Presenting Author: Anjan Dahal Presenter's Affiliation: Central Department of Physics, Tribhuvan University, Kathmandu, Nepal Title: Stopping Sites and Charge States of Muon in Azurin, Copper Protein Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Protein-mediated electron-transfer (ET) reactions are essential for converting energy in processes such as photosynthesis and respiration. For better understanding of the biological process, study of the ET mechanism is very important. Pioneered by K. Nagamine et al., ET in Cytochrome c protein [1], and DNA [2] reported using positive muon. To understand the muon experiment data, AD Pant et. al studied muon sites and charge state in amino acids and peptide bonds using first-principles calculations [3,4]. To understand ET in protein, we perform a systematic study to find stopping sites and charge states of muon in Azurin, Copper Protein.
Due to the complexity of biological system in geometry and dynamics, we have selected Azurin, which is a relatively small protein with copper as a single active site. We perform geometry optimization of structure and theoretical calculations using hybrid density functional (B3LYP/6-31G(d) and 6-31G(d,p)) in Gaussian 09 set of programs. Also, natural population analysis and electrostatic potential analysis helps to find the charge states and electronegative sites in the protein. Outcome of the research will provide valuable insights into the biochemistry and ET process in azurin and other big proteins. In the program, the stopping sites and charge states of muon in azurin will be presented.
References
[1] K. Nagamine et at., Physica B: Condensed Matter, 289 (2000) 631–635.
[2] E. Torikai et al., Hyperfine Interactions 138 (2001) 509–514.
[3] A. D. Pant et al., JPS Conf. Proc., 21 (2018) 011038.
[4] A. D. Pant et al., JPS Conf. Proc., 25 (2019) 011013.
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Abstract Number: ANPA2023-N00028 Presenting Author: Anup Shrestha Presenter's Affiliation: Central Department of Physics, Tribhuvan University, Kathmandu, Nepal Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Hypoxia, the region with low oxygen concentration in the tissue[1] is an important factor for tumor treatment. Since hypoxia causes resistance to the treatment [2], its detection is the foremost step towards the treatment process. Even though there are several existing methods to detect hypoxia, they come with limitations due to the requirement of special conditions and mainly due to invasive nature [3-5]. Instead, the newly proposed muon method does not require those special conditions and it is non-invasive in nature too, which is a great advantage over the currently existing methods[3,4]. Muon like a light proton, is more sensitive due to higher magnetic moment. Muonium, a bound state of muon and electron, is like a light isotope of hydrogen atom. In the proposed muon method, muonium undergoes spin exchange interaction with molecular oxygen to provide information about oxygen content in tumor tissue [3]. It is important to find the amount of muon beam dose to be used for the practical applications. Hence, we study the energy, intensity and profile (size) of the beam at various concentrations and sizes of the tumor. The estimated muon beam profile and energy using Monte Carlo simulation will be present in the program.
References
[1] W. C. Wilson and B. Shapiro, Anesthesiology Clinics of North America, 19 (2001) 769–812.
[2] P. Vaupel and L. Harrison, The oncologist, 9 (2004) 4–9.
[3] A. D. Pant et. al., Nuclear Instruments and Methods in Physics Research A, 1011 (2021) 165561.
[4] A. Pant et. al., Journal of Physics: Conference Series, 551 (2014) 012043.
[5] S. Chopra et. al., International journal of radiation biology, 85 (2009) 805–813.
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Abstract Number: ANPA2023-N00029 Presenting Author: Bidhya Thapa Presenter's Affiliation: Central Department of Physics, Tribhuvan University, Kathmandu, Nepal Title: Insights on the Interactions of Kaiso with p120 catenin from Molecular Simulations Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Protein-Protein interactions are crucial for the regulation of various cellular and biological processes. Molecular level insights on the interaction of Zinc finger (ZF) protein Kaiso with its binding partner p120 catenin are essential because of their role in development and cancers. Despite their important biological role, there is no structural characterization of the Kaiso-p120 catenin complex. In this work, we first modeled the optimum complex between Kaiso and p120 catenin through molecular docking and employed molecular dynamics (MD) simulations to investigate the structural features of this complex. Our MD simulation results show that the non contiguous 5’- and 3’- flanking regions of ZF domains in Kaiso interact with the 1-7 arm repeats of p120 catenin. The root mean square deviation (RMSD) measurements from the 500 ns of the MD simulation time reveal the stability of the Kaiso-p120 catenin complex. In addition, we identified the major interacting residues involved in the binding of these two proteins. Furthermore, we explored various non-covalent interactions such as; hydrogen bonds, salt-bridges, as well as hydrophobic interactions that are responsible for the complex formation and stabilization.
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Abstract Number: ANPA2023-N00026 Presenting Author: Narayan Gautam Presenter's Affiliation: Central Department of Physics, Kirtipur, Nepal Title: Molecular dynamics simulations-based investigation of HDAC7-MEF2A molecular interactions Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Molecular dynamics simulations-based investigation of HDAC7-MEF2A molecular interactions
Narayan Gautam1, Prem P. Chapagain2, Narayan P. Adhikari1, and Purushottam B. Tiwari3
Affiliations: 1Tribhuvan University, Kathmandu, Nepal; 2Florida International University, Mi-ami, FL, USA; 3Georgetown University, Washington, D.C., USA
Corresponding Email: chapagap@fiu.edu; narayan.adhikari@cdp.tu.edu.np; pbt7@georgetown.edu
Abstract
Interactions between histone deacetylase 7 (HDAC7) and myocyte enhancer factor 2 (MEF2) regulate MEF2 activity. In the past, experimental studies were carried out for the interactions between these proteins and determined range of amino acids that are responsible for interactions. Despite prior experimental studies, to the best of our knowledge, there are no investigations characterizing the complex formation leading to identification of amino acid residues. In this study, we first modelled the HDAC7-MEF2A complex using AlphaFold and then conducted molecular dynamics (MD) simulations of the complex. Our analysis of MD simulations trajectories explored key amino acid residues that are involved in the complex formation through different interactions.
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Abstract Number: ANPA2023-N00030 Presenting Author: Roshan Pudasaini Presenter's Affiliation: Kathmandu University Title: Muonium behavior in derivatives of Hemoglobin: a DFT study Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Muon is a spin-halved subatomic particle that can be found in cosmic rays (naturally) and accelerator facilities through pion decay. It has a mass that is around 207 times that of an electron and 1/9 that of a proton. Since the muon's gyromagnetic ratio is around three times greater than that of the proton, it is higher sensitive with respect to proton to magnetic field. Muon has two unique properties that make them unique tools: spin polarization and asymmetric decay to positron (caused by parity violation in weak contact). By stopping muons into the injected material, the local electronic and spin states of materials can be revealed through the muon spin rotation and relaxation (muSR) approach. Muonium on the other hand, is bound state of two lepton particles - positive muon and an electron with similar chemical properties of H atom. Muon method examines the local and dynamic state of spin, electron, proton, ions, and hydrogen in materials. It can also investigates phenomena based on these processes, such as electron transfer in the respiratory system, photosynthesis process, illness detection, clinical and medical fields, and reaction dynamics, catalytic processes, molecule concentration, magnetic behaviors etc.
In this study, the stopping site and charge states of muon and muonium in derivatives of hemoglobin have been studied through the first-principles approach. The stopping site of muon and muonium in derivatives of hemoglobin with extended main chain structure have been estimated.
The HOMO-LUMO gap and hyperfine coupling constant will be extracted from external files to understand the electronic states and interaction of muon with nearby nucleus.
By analyzing the stopping sites of muon and muonium within the hemoglobin structures, we aim to understand their preferential binding locations and the influence of molecular variations on their behavior. The obtained results shed light on the interactions between muon, muonium and the hemoglobin derivatives, revealing potential implications for their reactivity and functionality. Our DFT calculations not only contribute to the fundamental understanding of muon and muonium behavior in hemoglobin but also pave the way for further exploration of their interactions with other biomolecules. The findings from this study can potentially guide future experimental investigations and inspire the development of novel applications of muon in cancer research.
In the initial findings of the muonium behavior within the heme group of Deoxyhb, Oxyhb, and Cohb, we observed that the muonium tends to settle near the nitrogen atom of the pyrrole ring in the heme group. Conducting a theoretical analysis will be crucial in determining the precise location where the muon stops and the specific charge states it adopts in hemoglobin. This information will be invaluable in supporting the experimental investigation.
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Abstract Number: ANPA2023-N00031 Presenting Author: Roshan Pudasaini Presenter's Affiliation: Kathmandu University Title: Behavior of muon in derivatives of hemoglobin: a DFT study Location: Central Department of Physics, T.U., Nepal Show/Hide Abstract Behavior of muon in derivatives of hemoglobin: a DFT study
Roshan Pudasaini1, Amba Datt Pant2,3, Rajendra Prasad Adhikari1
1Kathmandu University, Dhulikhel, Kavre, Nepal,
2Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan,
3Muon Section, Materials and Life Science Division, J-PARC center, 2-4 Shirane Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
Email: roshanpudasaini879@gmail.com
There are various methods to detect low oxygen levels or hypoxia in tumor/cancer such as positron emission tomography, magnetic resonance imaging, electron paramagnetic resonance, and pulse oximetry with their limitations as mentioned by Tatum et al [1] and Conner et al [2]. A noninvasive technique is necessary to detect hypoxia and assess its existence, extent, and spatial distribution within a tumor. In order to develop a noninvasive tool for the diagnosis and treatment of cancer, we propose a muon method and detected the molecular oxygen in water and dilute aqueous biological solutions (Hb, TBS, albamin, serum)[3][4]. To interpret the muon experimental data, theoretical study is necessary to understand the stopping sites and charge states of injected muon into biomolecules. Here, we present density functional theory calculations to estimate the stopping sites, charge states and interaction of muon with nearby molecules in derivatives of hemoglobin.
Muon is a like a light proton with mass around 1/9 of that of a proton. Since the muon's gyromagnetic ratio is around three times greater than that of the proton, it has higher sensitivity with respect to proton to magnetic field. Muonium on the other hand, is bound state of two lepton particles - positive muon and an electron with similar chemical properties of H atom [5]. Relaxation rate of Mu due to spin exchange interaction with O2 provides the information about the existence of O2 in the solutions [6].
Based on minimum potential energy, we found the stopping site of the muonium in the heme group of DeoxyHb, OxyHb, and CoHb around the nitrogen atom of the imidazole ring of histidine. In the program, the precise locations of the muon with the specific charge states in derivatives of hemoglobin will be presented.
Reference:
[1] J. L. Tatum, Int. J. Radiat. Biol., 82 (2006) 699–757.
[2] J. P. O’Connor et al., Cancer Res., 76 (2016) 787–795.
[3] A. D. Pant et al., Nucl. Instrum. Methods Phys. Res. A, 1011 (2021) 165561.
[4] A. Pant et. al., Journal of Physics: Conference Series, 551 (2014) 012043.
[5]　K. Nagamine, Introductory muon science, Cambridge University Press, 2003.
[6]　A. D. Pant, J. Nepal Phys. Soc., 4 (2017) 7–10.
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Abstract Number: ANPA2023-N00092 Presenting Author: Vivek N. Prakash (Invited) Presenter's Affiliation: Department of Physics, University of Miami, Miami, FL Title: Fascinating Biophysics in Simple Marine Animals Location: Florida International University, FL, USA Show/Hide Abstract Animals are characterized by their movement, and their tissues are continuously subjected to dynamic force loading. Tissue mechanics determines the ecological niches that can be endured by a living organism. In the first part of my talk, I will present our surprising discovery of motility-induced tissue fractures and healing in a simple, early divergent marine animal – the Trichoplax adhaerens. I will demonstrate how fracture mechanics governs dramatic shape changes and asexual reproduction in this animal. In the second part of my talk, I will focus on the role of fluid mechanics in marine invertebrates. In starfish larvae, we discovered that ciliary arrays give rise to a beautiful pattern of slowly evolving vortices which determine a physical tradeoff between feeding and swimming.
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Abstract Number: ANPA2023-N00033 Presenting Author: Hugo Perez Presenter's Affiliation: Florida International University Title: Multimeric Assembly and Membrane Pore Forming Dynamics of the Lantibiotic Peptide Nisin Location: Florida International University, FL, USA Show/Hide Abstract Multidrug resistance in bacteria has led to a dire need for the development of new antibiotics with novel modes of action which can evade existing bacterial defenses. By targeting Lipid-II, antibiotic peptides such as Nisin disrupt bacteria’s ability to synthesize their cell wall. Lantibiotics bind to Lipid-II’s pyrophosphate moiety rather than the more commonly targeted peptide moiety. This means that bacteria that develop resistance to commercial antibiotics should still be vulnerable to lantibiotics. In this study, we use atomic-scale molecular dynamics computational studies to model stable oligomeric pore structures of nisin and investigate their dynamics and stability. We test a variety of conformations of nisin pore structures and motifs to find a viable structure. We also explore the role that Lipid-II plays in the formation and in maintaining the stability of the pores as well as the role transmembrane potentials play in the nature of the pores, including the channel volume and the ability of Nisin pores to exhibit ion selectivity.
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Abstract Number: ANPA2023-N00037 Presenting Author: Kyle J Cahill Presenter's Affiliation: Georgia State University Title: Connectivity in the Left Dorsal Stream is Enchanced in Video Gamers Location: Florida International University, FL, USA Show/Hide Abstract Video games provide sensory-rich, vision-dominated, competitive environments, in which players are continually challenged for moment-to-moment spatial navigation and decision-making. Recent studies have shown that video game players (gamers) enjoy the cognitive benefit of an increased reaction time, compared to non-gamers in making vision-based sensorimotor decisions. Hypotheses for how the brain processes visual information include the ‘two-streams’ model in which the visual pathway is bifurcated into dorsal and ventral streams. However, it is still unknown if video game playing can influence structural and functional changes in the visual streams of the brain. Here in this study, we examined the structural connectivity of the dorsal and ventral streams in gamers compared with non-gamers. After utilizing a Wilcoxson test on the metrics obtained from diffusion spectral imaging (DSI) analysis, we found that white matter tracts in the left dorsal stream between the left superior occipital gyrus and the left inferior parietal lobule were enhanced in video gamers indicated by elevated fractional anisotropy (FA) and normalized quantitative anisotropy (NQA) measures. The functional connectivity between the left superior occipital gyrus and the left superior parietal lobule was enhanced in video game players. Together the enhanced structural and functional connectivity within the left occipital-parietal regions in the visual stream may provide insight into the structural and functional basis for the beneficial effects of video game playing experience and may help explain the improved behavioral performance of video gamers in vision-based sensorimotor decision-making tasks.
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Abstract Number: ANPA2023-N00034 Presenting Author: Michael D. Cioffi Presenter's Affiliation: Florida International University Location: Florida International University, FL, USA Show/Hide Abstract The Ebola virus is a highly dangerous virus which can cause severe hemorrhagic fever in humans leading to high fatality rates. The Ebola virus matrix protein VP40 is the major protein responsible for the formation of the viral matrix by localizing and assembling it at the inner leaflet of the human plasma membrane (PM). This assembly leads to the formation of virus-like-particles (VLP) and eventual budding. Anionic lipids PI(4,5)P2 (PIP2) and Phosphatidylserine (PS) have been shown to facilitate VP40-PM binding through electrostatic interactions with cationic VP40 residues. It has been determined that Phosphatidic Acid (PA), resulting from the enzyme Phospholipase-D (PLD), may also play an active role in this process. We performed coarse-grained molecular dynamics (CGMD) simulations to investigate the effects various lipids have on VP40-lipid interactions. We used a triple-dimer structure of VP40 and a PM composed of various lipid types. Contact analyses show interactions with specific cationic VP40 residues that facilitate most of the lipid interactions. Interaction strengths between VP40 residues and lipid headgroups are found to vary when PA was included in the PM compared to when it was not. Radial distribution functions also show differences in local lipid clustering when PA was introduced into the PM. These simulations provide new insights on multi-dimer VP40 interactions with the human PM and how different lipid compositions may influence overall membrane association.
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Abstract Number: ANPA2023-N00035 Presenting Author: Santosh Khatri Presenter's Affiliation: Florida International University Location: Florida International University, FL, USA Show/Hide Abstract The behavior of individual molecules plays a crucial role in biochemical processes, which in turn influence the properties of cells and ultimately impact human behavior. Nanopore sensing, a cutting-edge technique for detecting and studying molecules at the single-molecule level, holds immense promise in unraveling the intricate details of molecular behavior. However, the sensitivity of existing nanopore methods, such as nanopipettes, is limited by the small size and fast speed of biomolecules. To address this problem, a novel approach of nanoconfinement at the nanopipette tip has been developed. This innovative method allows for the detection of smaller biomolecules, such as DNA bases and short peptides, using a nanopipette with a pore size over 10 times larger than the size of the biomolecule. The technique involves backfilling the nanopipette with biomolecules and then driving them out using concentration gradient and/or nanopore bias. This breakthrough enables deeper insights into the intermolecular interactions of various biomolecules and enables the detection of small single molecules at a scale of nearly 1 nanometer. In summary, the ability to detect and study small biomolecules with enhanced sensitivity using nanopipettes opens an exciting opportunity for understanding the intricate world of molecular behavior and has the potential to greatly impact fields such as drug discovery, personalized medicine, and biotechnology, opening new avenues for research and application in the field of molecular sciences.
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Abstract Number: ANPA2023-N00036 Presenting Author: Tej Kumar Sharma Presenter's Affiliation: Florida International University Location: Florida International University, FL, USA Show/Hide Abstract The emergence of the XBB.1.5 and XBB.1.16 subvariants of the omicron variant of SARS-CoV-2 has raised concern due to their transmissibility and potential impact on vaccine efficacy. These subvariants have been identified by the World Health Organization (WHO) as variants of concern (VOC). Here, we investigated the impact of the mutations in the structure of the receptor binding domain of the spike protein and its interactions with the host cell receptor ACE2. We found that the mutations enhance the RBD-ACE2 interactions in both subvariants. We also observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings suggest that these structural changes contributed to the subvariants' dominance over their predecessors, allowing for more rapid spread.
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Abstract Number: ANPA2023-N00032 Presenting Author: Yasir Mamun Presenter's Affiliation: Department of Chemistry and Biochemistry, Florida International University Location: Florida International University, FL, USA Show/Hide Abstract Human topoisomerase III beta (hTOP3B) is the only type IA topoisomerase in humans that works on both DNA and RNA substrates. This enzyme plays a crucial role in neurological development in mammals. Recently it has been found that hTOP3B is important for positive-sense single-stranded RNA viruses to replicate efficiently, making it a potential antiviral drug target. Although type IA topoisomerases of different organisms have been studied over the years, the step-by-step interaction of hTOP3B and nucleic acid substrates is still not elucidated. Molecular dynamics (MD) simulation is a tool for studying protein-substrate interaction, and we utilized this method to study the interactions between hTOP3B and nucleic acids. For this, we generated multiple models of hTOP3B complexed with DNA and RNA sequences using the hTOP3B crystal structure (PDB: 5GVC) and 8-mer single-stranded DNA and RNA sequences. These modeled complexes include both covalently and non-covalently complexed structures. We then performed MD simulations of all the modeled complexes. From the simulations, we can highlight the stability of the complexes, conformational changes, sequence preference, and interactions of the binding pocket residues with different nucleotides. Our work demonstrates that hTOP3B forms stable complexes with both RNA and DNA and highlights the suitability of the complexes for inhibitor discovery and binding study. It also provides a better understanding of the enzyme’s interaction with different nucleic acid substrate sequences.
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Abstract Number: ANPA2023-N00043 Presenting Author: Bhim M. Adhikari (Invited) Presenter's Affiliation: Maryland Psychiatry Research Center_x000D_ University of Maryland School of Medicine, Baltimore, USA Title: Resting state brain measures in healthy and patients population Location: Virtual Presentation Show/Hide Abstract The human brain is a complex organ, characterized with alterations/modifications, even too breakdowns, in the interaction patterns which are the hallmarks of diseased brains. In this talk, the speaker plans to introduce some of the resting state brain measures, network impairments and core cognitive deficits in schizophrenia, and comparison of these deficit patterns with the effects of drugs (ketamine and midazolam). In addition, cerebral blood flow and cardiovascular risk effects on resting brain regional homogeneity will be discussed. A brief summary of possible avenues for studying the human brain in health and disease will be provided.
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Abstract Number: ANPA2023-N00038 Presenting Author: Nawal khadka Presenter's Affiliation: Boise State University Location: Virtual Presentation Show/Hide Abstract Highly concentrated lens proteins, mostly crystallins, are responsible for maintaining the structure and refractivity of the eye lens. With increasing age, these crystallins form soluble and insoluble high molecular weight aggregates, which associate with lens membrane leading to lens hardening and cataract formation. The mechanism of such an association is still unclear. In this study, we explore the interaction of native β- and γ- crystallin extracted and purified from the cortex of the bovine lens with cholesterol (Chol)/phosphatidylcholine (PC) membrane with varying Chol content using atomic force microscopy (AFM). We prepared a supported lipid membrane by incubating small unilamellar vesicles (SUVs) on top of a freshly cleaved mica surface. Incubating β-crystallin on a defect-free membrane introduced locally modified semi-transmembrane defects, whereas γ- crystallins formed transmembrane defects on the phospholipid membrane. Rather than developing in multiple locations, the β-crystallin-induced defects expand in the localized area, whereas no significant increase in the size of transmembrane defect induced by γ- crystallin, was observed with increased incubation time. Our result shows that Chol inhibits the formation of membrane defects when β- and γ- crystallin interact with the Chol/PC membrane, and the degree of inhibition depends upon Chol content in the membrane. At a Chol/PC mixing ratio of 1, no defects were observed in membrane with γ- crystallin, whereas the severity of defects on membrane was decreased with β- crystallin. In conclusion, β- crystallin forms semi-transmembrane defects whereas γ- crystallin forms transmembrane defects when interacting with phospholipid membrane, and Chol suppresses the formation of such defects in the membrane. These results indicate the significance of Chol in the eye lens membrane in protecting against cataracts and lens hardening.
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Abstract Number: ANPA2023-N00040 Presenting Author: Jose I. Florentino Presenter's Affiliation: Department of Chemistry, Physics and Materials Science, Fayetteville State University, Fayetteville, North Carolina 28301, United States Location: Virtual Presentation Show/Hide Abstract DNA and RNA are similar but different from each other in terms of nitrogenous bases (Thymine versus Uracil), but to briefly explain, RNA is a single-stranded molecule with a short chain of nucleotides while DNA is a double-stranded molecule with a longer chain of nucleotides. These biological macromolecules replicate on their own from generation to generation. We investigate the vibrational spectra of both DNA and RNA strands analyzing the density of states (DOS) and dispersion curves within the framework of the harmonic Hamiltonian and Green’s function method. We reveal that the DNA and RNA molecules have band gaps making them possible candidates for biological sensors. Each model is investigated in three (infinite, finite, and cyclic) different configurations. We noticed that the models with lower symmetry show a large gap and a wide forbidden frequency range in all three configurations. The dispersion curves of the more symmetric model, namely the two channel double strands model, do not display the same large gap because its dispersion curves are highly degenerate. In the short DNA and RNA segments (finite and cyclic systems), there are more Van Hove singularities in the DOS curve.
Correspondence: cadhikari@uncfsu.edu (C.M. Adhikari)
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Abstract Number: ANPA2023-N00041 Presenting Author: Saniya L. Lyles Presenter's Affiliation: Department of Chemistry, Physics and Materials Science, Fayetteville State University, Fayetteville, North Carolina 28301, United States Title: Vibrational spectra of DNA and RNA Segments Location: Virtual Presentation Show/Hide Abstract Biological macromolecules Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) store and transmit genetic information from generation to generation. DNA and RNA are essential nucleic acids of all living organisms having the capacity to self-replicate. In the literature, various models are used to study DNA and RNA molecules. In this study, we model a DNA molecule as the four nitrogenous bases, namely adenine (A), cytosine (C), guanine (G), and thymine (T), connected by linear springs that vary in stiffness. The same for RNA molecules are the four nitrogenous bases, adenine (A), cytosine (C), guanine (G), and uracil (U), connected by linear springs with varying stiffness. Shorter pieces of modeled DNA and RNA structure have more "singularities," which create more bands in their density of states (DOS) plot, like those of infinite systems. As the length of these macromolecules and the number of parts increases, the impact of randomness on the way they move decreases, making the DOS plots more symmetrical.
This work is supported by the National Science Foundation RIA 1900998.
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Abstract Number: ANPA2023-N00042 Presenting Author: Amba Datt Pant Presenter's Affiliation: KEK/J-PARC, Japan Title: Muon in biology: applications in cancer research Location: Virtual Presentation Show/Hide Abstract Muon method (known as muon spin rotation, relaxation and resonance method, μSR method) is used to understand the local electronic and dynamic states of materials in which muon stops. In this method, we use quantum beam of muon available in accelerator facility (for some purposes, muons from cosmic ray are also used). Muon, a light proton, is a spin half particle with larger gyromagnetic ratio (around three times higher than that of proton) which makes it more sensitive to magnetic field in materials. Its bound state with an electron known as muonium (Mu = μ+e-) which is like a light isotope of hydrogen. For life sciences study, muon method can probe the dynamics of electron, proton, ions, H, O2, reaction, catalytic processes, concentration of molecules, magnetic behaviors, etc. and phenomena based on these processes (like electron transfer in respiratory system, photosynthesis process, diagnosis of disease, clinical and medical areas). We apply μSR method to understand electron transfer in proteins, and to visualize O2 in tumor to develop a noninvasive tool for diagnosis and treatment of life threating disease like cancer.
Low oxygen concentrations (called hypoxia) detection plays an important role in diagnosis/treatment of tumors [1] and cancer [2-3]. Even though there are some existing methods for the detection of molecular oxygen in tissues, new noninvasive methods to visualize hypoxic areas (extent and spatial distribution) in tumors of patients are still needed [2-4]. The oxygen concentration in human tumors is heterogeneous with some regions at low levels (less than 0.26 g/L of oxygen which is equivalent to less than 0.7% oxygen in gas phase) [5]. It is imperative to develop a tool/method to detect oxygen in the range from such a small concentration to normal oxygen level eventually in the human body especially in tissues in cancer patients.
Based on spin-exchange interaction between Mu and paramagnetic molecular oxygen, we have tested the sensitivity of the muon method for detection of O2 [6] and successfully detected O2 concentration in dilute biological aqueous solutions (solutions of Hb, albumin, serum and tris-buffered saline (TBS)) [7]. In the program, starting from an overview of muon in biology, our so far achievements and current status of systematic study towards the goal will be presented.
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Abstract Number: ANPA2023-N00039 Presenting Author: Olivia Walsh Presenter's Affiliation: California State Polytechnic University, Pomona Title: Direct Visualization of Antimicrobial Peptide - Induced Defects on Supported Lipid Bilayer Location: Virtual Presentation Show/Hide Abstract Antimicrobial peptides (AMPs) play a crucial role in the innate immune systems of various organisms. AMPs interact with bacterial and mammalian cell membranes through various mechanisms, varying from nanopore formation to microscale membrane lysis process. The interactions between AMPs and cell membranes have been studied extensively through various biochemical assays; they are thought to kill pathogens through cell membrane intervention. However, the mechanistic details behind membrane destabilization are still elusive. In this study, we used atomic force microscopy (AFM) to explore the effects of an AMP CM15 on model E. coli lipid membranes. CM15 is a hybrid peptide composed of Cecropin-A and melittin from bee venom. Our study sheds light on how CM15 interacts with a supported lipid bilayer.
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