A5037007496- Lipid Membrane Structure and Behavior
- Material Dynamics and Properties
- Force Microscopy Techniques and Applications
- Cellular transport and secretion
- Cellular Mechanics and Interactions
- Nanoparticle-Based Drug Delivery
- Protein Structure and Dynamics
- Monoclonal and Polyclonal Antibodies Research
- HER2/EGFR in Cancer Research
- Polymer Surface Interaction Studies
- Nanopore and Nanochannel Transport Studies
- DNA and Nucleic Acid Chemistry
- Theoretical and Computational Physics
- Mathematical Biology Tumor Growth
- Phase Equilibria and Thermodynamics
- Rheology and Fluid Dynamics Studies
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- DNA Repair Mechanisms
- Neuroblastoma Research and Treatments
- Computational Drug Discovery Methods
- Lung Cancer Treatments and Mutations
- Extracellular vesicles in disease
- nanoparticles nucleation surface interactions
- Microtubule and mitosis dynamics
University of Pennsylvania
2016-2025
California University of Pennsylvania
2014-2025
The University of Texas Medical Branch at Galveston
2022-2024
Centre College
2022
Philadelphia University
2015-2020
Translational Therapeutics (United States)
2013
University of Madras
2011
Bioengineering Center
2010
Courant Institute of Mathematical Sciences
2003-2006
National Institutes of Health
2006
We review the current state of knowledge phase separation and equilibria in porous materials. Our emphasis is on fundamental studies simple fluids (composed small, neutral molecules) well-characterized While theoretical molecular simulation are stressed, we also survey experimental investigations that nature. Following a brief most useful methods, describe nature gas-liquid (capillary condensation), layering, liquid-liquid freezing/melting transitions. In each case for pore geometries, more...
We present a review of experimental, theoretical, and molecular simulation studies confinement effects on freezing melting. consider both simple more complex adsorbates that are confined in various environments (slit or cylindrical pores also disordered porous materials). The most commonly used simulation, theoretical experimental methods first presented. provide brief description the widely materials. current state knowledge structure temperature, appearance new surface-driven...
ErbB3/HER3 is one of four members the human epidermal growth factor receptor (EGFR/HER) or ErbB tyrosine kinase family. ErbB3 binds neuregulins via its extracellular region and signals primarily by heterodimerizing with ErbB2/HER2/Neu. A recently appreciated role for in resistance tumor cells to EGFR/ErbB2-targeted therapeutics has made it a focus attention. However, efforts inactivate therapeutically parallel other receptors are challenging because intracellular domain thought be an...
Erlotinib and gefitinib, tyrosine kinase inhibitors used to block EGFR (epidermal growth factor receptor) signalling in cancer, are thought bind only the active conformation of EGFR-TKD (tyrosine domain). Through parallel computational crystallographic studies, we show present study that erlotinib also binds inactive conformation, which may have significant implications for its use EGFR-mutated cancers.
We use an order-parameter formulation, in conjunction with non-Boltzmann sampling to study the nucleation of clathrate hydrates from water–CO2 mixtures, using computer simulations. A set order parameters are defined: Φigg (i=1,2,…,n and gg for guest–guest), which characterize spatial orientational CO2 molecules, Φihh (hh host–host), govern ordering water molecules. These bond-orientational based on average geometrical distribution nearest-neighbor bonds. The free-energy hypersurface as a...
A computational methodology based on Metropolis Monte Carlo (MC) and the weighted histogram analysis method (WHAM) has been developed to calculate absolute binding free energy between functionalized nanocarriers (NC) endothelial cell (EC) surfaces. The calculated NC landscapes yield affinities that agree quantitatively when directly compared against analogous measurements of specific antibody-coated NCs (100 nm in diameter) intracellular adhesion molecule-1 (ICAM-1) expressing EC surface...
Abstract Activating point mutations in Anaplastic Lymphoma Kinase (ALK ) have positioned ALK as the only mutated oncogene tractable for targeted therapy neuroblastoma. Cells with these respond to lorlatinib pre-clinical studies, providing rationale a first-in-child Phase 1 trial (NCT03107988) patients ALK-driven To track evolutionary dynamics and heterogeneity of tumors, detect early emergence resistance, we collected serial circulating tumor DNA samples from enrolled on this trial. Here...
The massive amount of human biological, imaging, and clinical data produced by multiple diverse sources necessitates integrative modeling approaches able to summarize all this information into answers specific questions. In paper, we present a hypermodeling scheme combine models cancer aspects regardless their underlying method or scale. Describing tissue-scale cell proliferation, biomechanical tumor growth, nutrient transport, genomic-scale aberrant metabolism, cell-signaling pathways that...
Using molecular simulations and free energy calculations based on Landau theory, we show that freezing/melting behavior of fluids small molecules in pores simple geometry can be understood terms two main parameters: the pore width H* (expressed as a multiple diameter fluid molecule) parameter α measures ratio fluid-wall to fluid–fluid attractive interaction. The value determines qualitative nature freezing behavior, for example, direction change temperature presence or absence new phases....
We study the freezing of CCl4 in microporous activated carbon fibers (ACF), using Monte Carlo simulation and differential scanning calorimetry (DSC). Microporous are well characterized porous materials, having slit-shaped pores due to voids formed between graphitic basal planes. They serve as highly attractive adsorbents for simple nonpolar molecules, adsorbent–adsorbate interaction being mostly dispersive (of van der Waals-type). Recent molecular studies have predicted an upward shift...
We report molecular simulation studies of the freezing behavior fluids in nano-porous media. The effect confinement is to induce spatial constraints as well energetic heterogeneity on confined fluid, thereby altering bulk phase drastically. consider fluid-wall interaction energy shift temperature and fluid structure, using a novel approach calculate free surface based Landau theory order parameter formulation. Corresponding states then used map out global Lennard-Jones (LJ) model slit-shaped...
We report both experimental measurements and molecular simulations of the melting freezing behavior simple fluids in porous media. The studies are for carbon tetrachloride nitrobenzene controlled pore glass (CPG) Vycor. Differential scanning calorimetry (DSC) was used to determine point materials each samples. In case (which has a nonzero dipole moment), dielectric spectroscopy also points. Measurements by two methods were excellent agreement. found be depressed relative bulk value fluids....
We report a molecular simulation study of freezing transitions for simple fluids in narrow slit pores. A major stumbling block previous studies pores has been the lack any method calculating free energy difference between confined solid and liquid phases. Conventional thermodynamic integration methods often fail systems, due to difficulty choosing suitable path integration. use different approach that involves Landau as function order parameter, using grand canonical Monte Carlo method. The...
Our application of transition path sampling to a complex biomolecular system in explicit solvent, the closing DNA polymerase β, unravels atomic and energetic details conformational change that precedes chemical reaction nucleotide incorporation. The computed profile offers detailed mechanistic insights into, as well kinetic information on, process essential for synthesis repair. five identified states extend available experimental modeling data by revealing highly cooperative dynamics...
Targeting nanoparticles (NPs) loaded with drugs and probes to precise locations in the body may improve treatment detection of many diseases. Generally, achieve targeting, affinity ligands are introduced on surface NPs that can bind molecules present cell interest. Optimization ligand density is a critical parameter controlling NP binding target cells, higher not always most effective. In this study, we investigated how avidity affects targeting pulmonary vasculature, using targeted ICAM-1....
We report both experimental measurements and molecular simulations of the melting freezing behavior fluids in nanoporous media. The studies are for nitrobenzene silica-based pores controlled pore glass, Vycor, MCM-41. Dielectric relaxation spectroscopy is used to determine points orientational times molecules bulk confined phase. Monte Carlo simulations, together with a bond order parameter method, point fluid structure inside cylindrical modeled on silica. Qualitative comparison between...
The process by which supercooled fluids form stable, crystalline solids has been found to be elusive both experimentally and via computer simulations. This is because this process, generally called nucleation, statistical in nature the set of intermediate states, critical nucleus, very short-lived. Thus, there are large uncertainties even limited experimental data that exist, simulations have performed can yield descriptive information at best. Here we present a detailed quantitatively...
We report molecular simulation studies of the diffusion processes in ice and CO2 clathrate hydrates performed using classical potential models water (SPC/E) carbon dioxide (EPM2). The diffusivity H2O is calculated to be 1.3×10−18 m2 s−1 at 200 K dynamics simulations, a result good agreement with experimental data. also computed both Monte Carlo simulations together Landau free energy method. barriers for hopping between cages without defect present. determined that vacancy was necessary CO2,...