Related papers: Optimized Baxter Model of Protein Solutions: Elect…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
In this work 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate (CMA2OEM) molecule has been characterized theoretically. First, the potential energy surface has been calculated to find the lowest energy state of the molecule. After the most…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
We formulate a class of velocity-free finite-particle methods for mass transport problems based on a time-discrete incremental variational principle that combines entropy and the cost of particle transport, as measured by the Wasserstein…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
We present the derivation of second-order relativistic viscous hydrodynamics from an effective Boltzmann equation for a system consisting of quasiparticles of a single species. We consider temperature-dependent masses of the quasiparticles…
Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Using the density functional formalism we derive expression for the distortion free energy for systems with continuous broken symmetry and use it to derive expression for the elastic constants of smectic phases in which director is tilted…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Optical tweezers are powerful tools for high resolution study of surface properties. Such experiments are traditionally performed by studying the active or the brownian fluctuation of trapped particles in the X, Y, Z direction. Here we find…
We present a first-principles-based (second-principles) scheme that permits large-scale materials simulations including both atomic and electronic degrees of freedom on the same footing. The method is based on a predictive…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
Emerging coherent X-ray scattering patterns of single particles have shown dominant morphological signatures in agreement with predictions of the scattering model used for conventional protein crystallography. The key question is if and to…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…