Related papers: Probing protein orientation near charged nanosurfa…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
The possibility to control electrokinetic transport through carbon and hexagonal boron nitride (hBN) nanotubes has recently opened new avenues for nanofluidic approaches to face outstanding challenges such as energy production and…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Surface sensitive synchrotron x-ray scattering studies were performed to obtain the distribution of monovalent ions next to a highly charged interface. A lipid phosphate (dihexadecyl hydrogen-phosphate) was spread as a monolayer at the…
Photoresponse of bimetallic Au-Ag nanoparticle embedded soda glass (Au-Ag@SG) substrate is reported for surface plasmon assisted optical switching using 808 nm excitation. Au-Ag@SG system is made by an ion beam technique where Ag^+ is…
Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustration, two case studies are presented. In the first case, a…
Proteins belonging to immunoglobulin superfamily(IgSF) show remarkably conserved nature both in their folded structure and in their folding process, but they neither originate from very similar sequences nor demonstrate functional…
The initiation of intergranular corrosion at various types of grain boundaries (GBs) was studied at the nanometer scale on microcrystalline copper in 1 mM HCl aqueous solution. In situ Electrochemical Scanning Tunneling Microscopy (ECSTM)…
Nanoparticles usually exhibit pronounced anisotropic properties, and a close insight into the atomic-scale deformation mechanisms is of great interest. In present study, atomic simulations are conducted to analyze the compression of bcc…
We have earlier reported the iMOLSDOCK technique to perform induced-fit peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLS) technique to sample the conformation and the docking pose of the small molecule…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
We study the low-temperature behavior and the phase transition of a thin film by Monte Carlo simulation. The thin film has a simple cubic lattice structure where each site is occupied by a Potts parameter which indicates the molecular…
Laser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with x-ray free-electron lasers [PRL 92, 198102 (2004)]. However, the alignment…
We study protein diffusion in multicomponent lipid membranes close to a rigid substrate separated by a layer of viscous fluid. The large-distance, long-time asymptotics for Brownian motion are calculated using a nonlinear stochastic…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…