Biomolecules
We present an algorithm to estimate the configurational entropy $S$ of a polymer. The algorithm uses the statistics of coincidences among random samples of configurations and is related to the catch-tag-release method for estimation of…
Gaussian network model (GNM) is one of the most accurate and efficient methods for biomolecular flexibility analysis. However, the systematic generalization of the GNM has been elusive. We show that the GNM Kirchhoff matrix can be built…
We consider a single-species diffusion-limited annihilation reaction with reactants confined to a two-dimensional surface with one arbitrarily large dimension and the other comparable in size to interparticle distances. This situation could…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
Prion diseases {\it (e.g. Creutzfeldt-Jakob disease (CJD), variant CJD (vCJD), Gerstmann-Str$\ddot{\text{a}}$ussler-Scheinker syndrome (GSS), Fatal Familial Insomnia (FFI) and Kuru in humans, scrapie in sheep, bovine spongiform…
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms…
We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
The electronic structure of charybdotoxin (ChTX), a scorpion venom peptide that is known to act as a potassium channel blocker, is investigated with the aid of quantum mechanical calculations. The dipole moment vector (145 D) of ChTX can be…
Here we propose the approach to design of the new type of hybrids of oligonucleotides with fluorescein-functionalized single-walled carbon nanotubes. The approach is based on stacking interactions of functionalized nanotubes with pyrene…
Voltage-gated ion channels mediate electrical excitability of cellular membranes. Reduced models of the voltage sensor (VS) of Kv channels produce insight into the electrostatic physics underlying the response of the highly positively…
Electrical signaling via voltage-gated ion channels depends upon the function of the voltage sensor (VS), identified with the S1-S4 domain of voltage-gated K channels. Here we investigate some physical aspects of the sliding-helix model of…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Allosteric communication in proteins is a central and yet unsolved problem of structural biochemistry. Previous findings, from computational biology (Ota and Agard, 2005), have proposed that heat diffuses in a protein through cognate…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
We present a dual optimization concept of predicting optimal sequences as well as optimal folds of off-lattice protein models in the context of multi-scale modeling. We validate the utility of the recently introduced hidden-force Monte…
During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively…