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Biological and Chemical Physics

2013

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Articles 1 - 30 of 32

Full-Text Articles in Physics

Hydrogen Evolution Reaction Measurements Of Dealloyed Porous Nicu, Kyla Koboski, Evan Nelsen, Jennifer R. Hampton Dec 2013

Hydrogen Evolution Reaction Measurements Of Dealloyed Porous Nicu, Kyla Koboski, Evan Nelsen, Jennifer R. Hampton

Faculty Publications

Porous metals are of interest for their high surface area and potential for enhanced catalytic behavior. Electrodeposited NiCu thin films with a range of compositions were electrochemically dealloyed to selectively remove the Cu component. The film structure, composition, and reactivity of these samples were characterized both before and after the dealloying step using scanning electron microscopy, energy-dispersive spectroscopy, and electrochemical measurements. The catalytic behavior of the dealloyed porous Ni samples towards the hydrogen evolution reaction was measured and compared to that of the as-deposited samples. The dealloyed samples were generally more reactive than their as-deposited counterparts at low overpotentials, making ...


Mechanisms Of Hemolysis-Associated Platelet Activation, Christine C. Helms, M. Marvel, W. Zhao, M. Stahle, R. Vest, G. J. Kato, J. S. Lee, G. Christ, M. T. Gladwin, R. R. Hantgan, D. B. Kim-Shapiro Dec 2013

Mechanisms Of Hemolysis-Associated Platelet Activation, Christine C. Helms, M. Marvel, W. Zhao, M. Stahle, R. Vest, G. J. Kato, J. S. Lee, G. Christ, M. T. Gladwin, R. R. Hantgan, D. B. Kim-Shapiro

Physics Faculty Publications

Background

Intravascular hemolysis occurs after blood transfusion, in hemolytic anemias, and in other conditions, and is associated with hypercoagulable states. Hemolysis has been shown to potently activate platelets in vitro and in vivo, and several mechanisms have been suggested to account for this, including: (i) direct activation by hemoglobin (Hb); (ii) increase in reactive oxygen species (ROS); (iii) scavenging of nitric oxide (NO) by released Hb; and (iv) release of intraerythrocytic ADP.

Objective

To elucidate the mechanism of hemolysis-mediated platelet activation.

Methods

We used flow cytometry to detect PAC-1 binding to activated platelets for in vitro experiments, and a Siemens ...


Interactive Wireless Sensor For Remote Trace Detection And Recognition Of Hazardous Gases, Audrey Lama Dec 2013

Interactive Wireless Sensor For Remote Trace Detection And Recognition Of Hazardous Gases, Audrey Lama

Masters Theses & Specialist Projects

The interactive wireless sensor detects many hazardous gases such as Hexane, Propane, Carbon monoxide and Hydrogen. These gases are highly toxic and used in different kinds of manufacturing industries, domestic purpose and so on. So, building a sensor that can detect this kind of gases can save the environment; prevent the potential for explosion, and endangering human life. In long term, interactive wireless sensor can also prevent the financial losses that might occur due to the hazardous incident that might occur due to these toxic gases.

Hexane is a colorless, strong gas which inhaled in significant amounts by a person ...


Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov Nov 2013

Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov

Publications

Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions, and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies which illustrate the association between missense mutations and diseases. In addition we ...


Solution Scattering And Fret Studies Of Nucleosomes Reveal Dna: Unwrapping Effects Of H3 And H4 Tail Removal, Kurt Andresen, Isabel Jimenez-Useche, Steven C. Howell, Chongli Yuan, Xiangyun Qiu Nov 2013

Solution Scattering And Fret Studies Of Nucleosomes Reveal Dna: Unwrapping Effects Of H3 And H4 Tail Removal, Kurt Andresen, Isabel Jimenez-Useche, Steven C. Howell, Chongli Yuan, Xiangyun Qiu

Physics and Astronomy Faculty Publications

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes ...


Investigating The Effect Of Characteristic X-Rays In Cadmium Zinc Telluride Detectors Under Breast Computerized Tomography Operating Conditions, Stephen J. Glick, Clay Didier Oct 2013

Investigating The Effect Of Characteristic X-Rays In Cadmium Zinc Telluride Detectors Under Breast Computerized Tomography Operating Conditions, Stephen J. Glick, Clay Didier

University of Massachusetts Medical School Faculty Publications

A number of research groups have been investigating the use of dedicated breast computerized tomography (CT). Preliminary results have been encouraging, suggesting an improved visualization of masses on breast CT as compared to conventional mammography. Nonetheless, there are many challenges to overcome before breast CT can become a routine clinical reality. One potential improvement over current breast CT prototypes would be the use of photon counting detectors with cadmium zinc telluride (CZT) (or CdTe) semiconductor material. These detectors can operate at room temperature and provide high detection efficiency and the capability of multi-energy imaging; however, one factor in particular that ...


Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, Yu-Qi Li, Xiao-Yin Pan, Viraht Sahni Sep 2013

Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, Yu-Qi Li, Xiao-Yin Pan, Viraht Sahni

Publications and Research

The many-body wave function of a system of interacting particles confined by a time-dependent harmonic potential and perturbed by a time-dependent spatially homogeneous electric field is derived via the Feynman path-integral method. The wave function is comprised of a phase factor times the solution to the unperturbed time-dependent Schrödinger equation with the latter being translated by a time-dependent value that satisfies the classical driven equation of motion. The wave function reduces to that of the Harmonic Potential Theorem wave function for the case of the time-independent harmonic confining potential.


Experimental Microwave Breast Cancer Detection With Oil-On-Gelatin Phantom, Giuseppe Ruvio, Raffaele Solimene, Antonio Cuccaro, Jacinta Browne, Domenico Gaetano, Max Ammann Sep 2013

Experimental Microwave Breast Cancer Detection With Oil-On-Gelatin Phantom, Giuseppe Ruvio, Raffaele Solimene, Antonio Cuccaro, Jacinta Browne, Domenico Gaetano, Max Ammann

Conference Papers

Limitations of conventional X-ray mammography has induced a recent interest into radio frequency based diagnostic approaches in order to take advantage of the sharpest dielectric contrast between benign and malignant breast tissues in the microwave frequency range [1]. Dielectric contrast is notably higher than the radiographic density exploited by X-ray mammography. Consequences of the superior sensitivity of RF-based techniques can have a huge social and cost impact. By reducing the false response percent, a dramatic reduction of costs for the health system together with a diminution of traumatic experiences for the patients can be achieved. The antenna properties play a ...


Hemoglobin-Mediated Nitric Oxide Signaling, Christine C. Helms, D. B. Kim-Shapiro Aug 2013

Hemoglobin-Mediated Nitric Oxide Signaling, Christine C. Helms, D. B. Kim-Shapiro

Physics Faculty Publications

The rate that hemoglobin reacts with nitric oxide (NO) is limited by how fast NO can diffuse into the heme pocket. The reaction is as fast as any ligand/protein reaction can be and the result, when hemoglobin is in its oxygenated form, is formation of nitrate in what is known as the dioxygenation reaction. As nitrate, at the concentrations made through the deoxygenation reaction, is biologically inert, the only role hemoglobin was once thought to play in NO signaling was to inhibit it. However, there are now several mechanisms that have been discovered by which hemoglobin may preserve, control ...


Ion Competition In Condensed Dna Arrays In The Attractive Regime, Xiangyun Qiu, John Giannini, Steven C. Howell, Qi Xia, Fuyou Ke, Kurt Andresen Aug 2013

Ion Competition In Condensed Dna Arrays In The Attractive Regime, Xiangyun Qiu, John Giannini, Steven C. Howell, Qi Xia, Fuyou Ke, Kurt Andresen

Physics and Astronomy Faculty Publications

Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt3+ Hexammine, or Co3+Hex) and one nonDNA-condensing ion (Mg2+) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are ...


An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez Jul 2013

An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez

FIU Electronic Theses and Dissertations

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the ...


Elucidating Internucleosome Interactions And The Roles Of Histone Tails, Steven C. Howell, Kurt Andresen, Isabel Jimenez-Useche, Chongli Yuan, Xiangyun Qiu Jul 2013

Elucidating Internucleosome Interactions And The Roles Of Histone Tails, Steven C. Howell, Kurt Andresen, Isabel Jimenez-Useche, Chongli Yuan, Xiangyun Qiu

Physics and Astronomy Faculty Publications

The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range and guided by specific contacts at short range, particularly involving their flexible histone tails. We have thus quantified how internucleosome interactions are modulated by salts (KCl, MgCl2) and histone tail deletions (H3, H4 N-terminal), using small-angle x-ray scattering and theoretical modeling. We found that measured effective charges at low salts are ∼1/5th of the theoretically predicted renormalized charges and that H4 tail deletion ...


Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov Jun 2013

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6 ...


Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko Jun 2013

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical ...


Raman Spectroscopic Analysis Of Human Skin Tissue Sections Ex-Vivo: Evaluation Of The Effects Of Tissue Processing And Dewaxing, Syed Mehmood Ali, Franck Bonnier, Ali Tfayli, Helen Lambkin, Kathleen Flynn, Vincent Mcdonagh, Claragh Healy, Thomas Lee, Fiona Lyng, Hugh Byrne Jun 2013

Raman Spectroscopic Analysis Of Human Skin Tissue Sections Ex-Vivo: Evaluation Of The Effects Of Tissue Processing And Dewaxing, Syed Mehmood Ali, Franck Bonnier, Ali Tfayli, Helen Lambkin, Kathleen Flynn, Vincent Mcdonagh, Claragh Healy, Thomas Lee, Fiona Lyng, Hugh Byrne

Articles

Raman spectroscopy coupled with K-means clustering analysis (KMCA) is employed to elucidate the biochemical structure of human skin tissue sections, and the effects of tissue processing. Both hand and thigh sections of human cadavers were analysed in their unprocessed and formalin fixed paraffin processed (FFPP) and subsequently dewaxed forms. In unprocessed sections, KMCA reveals clear differentiation of the stratum corneum, intermediate underlying epithelium and dermal layers for sections from both anatomical sites. The stratum corneum is seen to be relatively rich in lipidic content; the spectrum of the subjacent layers is strongly influenced by the presence of melanin, while that ...


The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov May 2013

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of ...


Biophysical Characterization Of Optimized Self-Assembling Protein Nanoparticles As A Malaria Vaccine, Sophia Walker May 2013

Biophysical Characterization Of Optimized Self-Assembling Protein Nanoparticles As A Malaria Vaccine, Sophia Walker

Honors Scholar Theses

Malaria is an infectious disease that affects several million individuals worldwide and is a significant international public health issue. While there is currently a malaria vaccine in phase III clinical trials, recent results demonstrate that it is only about 35% effective in reducing the incidence of the disease. The use of self-assembling protein nanoparticles (SAPNs) that display epitopes of the repeat sequence of the circumsporozoite protein of Plasmodium falciparum, the parasite that causes malaria, has been shown to elicit a strong immune response. This prototype has potential for further improvement by altering the epitope regions of the nanoparticles to be ...


Novel Materials For Use In Homeland Security Research, Jason Osgood Ewen Young May 2013

Novel Materials For Use In Homeland Security Research, Jason Osgood Ewen Young

Masters Theses & Specialist Projects

Organometallic pyridazines and compounds derived from them have been of interest in polymer research due to their atypical environmental stability (as compared to other non-aromatic organic semiconductors) as well as their conductivity. The off-metal synthesis and characterization of several pyridazyl thallium, manganese, and rhenium complexes, beginning with fulvenes 1,2- C5H3(COHR)(COR), are reported here. The diacyl fulvenes were treated with hydrazine hydrate to ring close to pyridazines. Next, the pyridazines were converted to their respective thallium salts through treatment with thallium (I) ethoxide. Lastly, the salts were transmetallated into the respective rhenium or manganese complexes through treatment with ...


Enhanced Nucleate Boiling On Horizontal Hydrophobic-Hydrophilic Carbon Nanotube Coatings, Xianming Dai, Xinyu Huang, Fanghao Yang, Xiaodong Li, Joshua Sightler, Yingchao Yang, Chen Li Apr 2013

Enhanced Nucleate Boiling On Horizontal Hydrophobic-Hydrophilic Carbon Nanotube Coatings, Xianming Dai, Xinyu Huang, Fanghao Yang, Xiaodong Li, Joshua Sightler, Yingchao Yang, Chen Li

Faculty Publications

Ideal hydrophobic-hydrophilic composite cavities are highly desired to enhance nucleate boiling. However, it is challenging and costly to fabricate these types of cavities by conventional micro/nano fabrication techniques. In this study, a type of hydrophobic-hydrophilic composite interfaces were synthesized from functionalized multiwall carbon nanotubes by introducing hydrophilic functional groups on the pristine multiwall carbon nanotubes. This type of carbon nanotube enabled hydrophobic-hydrophilic composite interfaces were systematically characterized. Ideal cavities created by the interfaces were experimentally demonstrated to be the primary reason to substantially enhance nucleate boiling


Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier Apr 2013

Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier

Bioelectrics Publications

Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that ...


Ultraviolet Photodissociation Of Ocs: Product Energy And Angular Distributions, George C. Mcbane, Johan A. Schmidt, M. S. Johnson, Reinhard Schinke Mar 2013

Ultraviolet Photodissociation Of Ocs: Product Energy And Angular Distributions, George C. Mcbane, Johan A. Schmidt, M. S. Johnson, Reinhard Schinke

Peer Reviewed Articles

The ultraviolet photodissociation of carbonyl sulfide (OCS) was studied using three-dimensional potential energy surfaces and both quantum mechanical dynamics calculations and classical trajectory calculations including surface hopping. The transition dipole moment functions used in an earlier study [J. A. Schmidt, M. S. Johnson, G. C. McBane, and R. Schinke, J. Chem. Phys. 137, 054313 (2012)] were improved with more extensive treatment of excited electronic states. The new functions indicate a much larger contribution from the 1 1A" state (1Σ- in linear OCS) than was found in the previous work. The new transition dipole functions yield absorption spectra that ...


Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov Mar 2013

Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov

Publications

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to ...


A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov Feb 2013

A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov

Publications

BACKGROUND AND SIGNIFICANCE:

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE:

To reveal the molecular mechanisms of various intellectual disabilities and to ...


Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov Feb 2013

Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

Publications

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report ...


Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia Jan 2013

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric ...


Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia Jan 2013

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output ...


Controlling Reactivity Of Nanoporous Catalyst Materials By Tuning Reaction Product-Pore Interior Interactions: Statistical Mechanical Modeling, Jing Wang, David M. Ackerman, Victor S.-Y. Lin, Marek Pruski, James W. Evans Jan 2013

Controlling Reactivity Of Nanoporous Catalyst Materials By Tuning Reaction Product-Pore Interior Interactions: Statistical Mechanical Modeling, Jing Wang, David M. Ackerman, Victor S.-Y. Lin, Marek Pruski, James W. Evans

Physics and Astronomy Publications

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction ...


Atomistic Modeling Of The Directed-Assembly Of Bimetallic Pt-Ru Nanoclusters On Ru(0001)-Supported Monolayer Graphene, Yong Han, Albert K. Engstfeld, R. Juergen Behm, James W. Evans Jan 2013

Atomistic Modeling Of The Directed-Assembly Of Bimetallic Pt-Ru Nanoclusters On Ru(0001)-Supported Monolayer Graphene, Yong Han, Albert K. Engstfeld, R. Juergen Behm, James W. Evans

Physics and Astronomy Publications

The formation of Pt-Ru nanoclusters (NCs) by sequential deposition of Pt and Ru on a periodically rumpled graphene sheet supported on Ru(0001) is analyzed by atomistic-level modeling and kinetic Monte Carlo simulations. The “coarse-scale” periodic variation of the adsorption energy of metal adatoms across the graphene sheet directs the assembly of NCs to a periodic array of thermodynamically preferred locations. The modeling describes not only just the NC densities and size distributions, but also the composition distribution for mixed NCs. A strong dependence of these quantities on the deposition order is primarily related to different effective mobilities of Pt ...


In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov Jan 2013

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed ...


Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov Jan 2013

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to ...