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Articles 1 - 13 of 13
Full-Text Articles in Physics
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Chemistry: Faculty Publications and Other Works
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …
Experimental Evidence That Metapopulation Structure Can Accelerate Adaptive Evolution, Partha Pratim Chakraborty, Louis R. Nemzer, Rees Kassen
Experimental Evidence That Metapopulation Structure Can Accelerate Adaptive Evolution, Partha Pratim Chakraborty, Louis R. Nemzer, Rees Kassen
Chemistry and Physics Faculty Articles
Whether the spatial arrangement of a population influences adaptive evolution has been a long-standing question in population genetics. In contrast to standard population genetic models, evolutionary graph theory (EGT) predicts certain topologies amplify (increase) the probability that a beneficial mutation will spread in the population relative to a well-mixed population. Here, we test these predictions empirically by tracking the fixation dynamics of an antibiotic resistant mutant under positive selection as it spreads through networks of different topologies both in vitro and in silico. We show that star-like topologies involving bi-directional dispersal between a central hub and peripheral leaves can …
Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei
Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei
Mathematics Faculty Publications
While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …
Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye
Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye
Biology: Faculty Publications and Other Works
Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …
Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner
Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner
Publications and Research
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …
The Biomechanics Of The Softball Swing In Seven Stages: Optimizing Exit Velocity, Ceara A. Larson
The Biomechanics Of The Softball Swing In Seven Stages: Optimizing Exit Velocity, Ceara A. Larson
Lawrence University Honors Projects
The study of sports biomechanics is a rapidly developing field that can be used to analyze an athlete’s most critical motions and improve their performance. In the world of baseball, sports biomechanists, scientists dedicated to the field of sports biomechanics, help keep pitchers healthy, optimize pitch performance, and improve a batter’s swing efficiency. Because of their surface-level similarities, the findings of baseball biomechanical studies have been projected onto the sport of women’s fastpitch softball, despite their substantial differences in physiology, field dimensions, pitch delivery, and classifications of hitters. The purpose of this study is to produce a biomechanical analysis unique …
Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea
Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea
Physics Faculty Publications and Presentations
Liposomes are spherical-shaped vesicles that enclose an aqueous milieu surrounded by bilayer or multilayer membranes formed by self-assembly of lipid molecules. They are intensively exploited as either model membranes for fundamental studies or as vehicles for delivery of active substances in vivo and in vitro. Irrespective of the method adopted for production of loaded liposomes, obtaining the final purified product is often achieved by employing multiple, time consuming steps. To alleviate this problem, we propose a simplified approach for concomitant production and purification of loaded liposomes by exploiting the Electrodialysis-Driven Depletion of charged molecules from solutions. Our investigations show that …
Cholesterol And Cholesterol Bilayer Domains Inhibit Binding Of Alpha-Crystallin To The Membranes Made Of The Major Phospholipids Of Eye Lens Fiber Cell Plasma Membranes, Raju Timsina, Geraline Trossi-Torres, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali
Cholesterol And Cholesterol Bilayer Domains Inhibit Binding Of Alpha-Crystallin To The Membranes Made Of The Major Phospholipids Of Eye Lens Fiber Cell Plasma Membranes, Raju Timsina, Geraline Trossi-Torres, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali
Physics Faculty Publications and Presentations
The concentration of α-crystallin decreases in the eye lens cytoplasm, with a corresponding increase in membrane-bound α-crystallin during cataract formation. The eye lens’s fiber cell plasma membrane consists of extremely high cholesterol (Chol) content, forming cholesterol bilayer domains (CBDs) within the membrane. The role of high Chol content in the lens membrane is unclear. Here, we applied the continuous-wave electron paramagnetic resonance spin-labeling method to probe the role of Chol and CBDs on α-crystallin binding to membranes made of four major phospholipids (PLs) of the eye lens, i.e., phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylserine (PS), and phosphatidylethanolamine (PE). Small unilamellar vesicles …
Liposomes Prevent In Vitro Hemolysis Induced By Streptolysin O And Lysenin, Marcelo Ayllon, Gamid Abatchev, Andrew Bogard, Rosey Whiting, Sarah E. Hobdey, Daniel Fologea
Liposomes Prevent In Vitro Hemolysis Induced By Streptolysin O And Lysenin, Marcelo Ayllon, Gamid Abatchev, Andrew Bogard, Rosey Whiting, Sarah E. Hobdey, Daniel Fologea
Physics Faculty Publications and Presentations
The need for alternatives to antibiotics in the fight against infectious diseases has inspired scientists to focus on antivirulence factors instead of the microorganisms themselves. In this respect, prior work indicates that tiny, enclosed bilayer lipid membranes (liposomes) have the potential to compete with cellular targets for toxin binding, hence preventing their biological attack and aiding with their clearance. The effectiveness of liposomes as decoy targets depends on their availability in the host and how rapidly they are cleared from the circulation. Although liposome PEGylation may improve their circulation time, little is known about how such a modification influences their …
Investigating The Use Of Ultraviolet Light Emitting Diodes (Uv-Leds) For The Inactivation Of Bacteria In Powdered Food Ingredients, Laura Nyhan, Milosz Przyjalgowski, Liam O'Faolain, Máire Begley, Michael Callanan
Investigating The Use Of Ultraviolet Light Emitting Diodes (Uv-Leds) For The Inactivation Of Bacteria In Powdered Food Ingredients, Laura Nyhan, Milosz Przyjalgowski, Liam O'Faolain, Máire Begley, Michael Callanan
Cappa Publications
The addition of contaminated powdered spices and seasonings to finished products which do not undergo further processing represents a significant concern for food manufacturers. To reduce the incidence of bacterial contamination, seasoning ingredients should be subjected to a decontamination process. Ultraviolet light emitting diodes (UV-LEDs) have been suggested as an alternative to UV lamps for reducing the microbial load of foods, due to their increasing efficiency, robustness and decreasing cost. In this study, we investigated the efficacy of UV-LED devices for the inactivation of four bacteria (Listeria monocytogenes, Escherichia coli, Bacillus subtilis and Salmonella Typhimurium) on a plastic surface and …
Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne
Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne
Articles
Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) …
Acoustic Communication In The Atlantic Mudskipper, Periopthalmus Barbarus, Seth Hoffman
Acoustic Communication In The Atlantic Mudskipper, Periopthalmus Barbarus, Seth Hoffman
Mahurin Honors College Capstone Experience/Thesis Projects
Mudskippers are intertidal fishes that can survive both in and out of the water. They are territorial and exhibit behaviors to attract mates and defend against competitors. Recently, it has been shown that vibrations are produced and transmitted through the mud during such displays in one species, Periophthalmodon septemradiatus. To see if similar vibrations are produced in other species of mudskippers, I recorded the behavioral interactions of pairs of the mudskipper Periophthalmus barbarus via digital video and acoustic signals via accelerometer. Comparative analysis of fish mass, sex, contest length, and contest outcome coupled with acoustic characteristics within dyadic pairings …
The Resistive Barrier Discharge: A Brief Review Of The Device And Its Biomedical Applications, Mounir Laroussi
The Resistive Barrier Discharge: A Brief Review Of The Device And Its Biomedical Applications, Mounir Laroussi
Electrical & Computer Engineering Faculty Publications
This paper reviews the principles behind the design and operation of the resistive barrier discharge, a low temperature plasma source that operates at atmospheric pressure. One of the advantages of this plasma source is that it can be operated using either DC or AC high voltages. Plasma generated by the resistive barrier discharge has been used to efficiently inactivate pathogenic microorganisms and to destroy cancer cells. These biomedical applications of low temperature plasma are of great interest because in recent times bacteria developed increased resistance to antibiotics and because present cancer therapies often are accompanied by serious side effects. Low …