Related papers: Macromolecular unfolding properties in presence of…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
The influence of hydroxyectoine on the properties of the aqueous solution in presence of DPPC lipid bilayers is studied via semi-isotropic constant pressure (NPT) Molecular Dynamics simulations. We investigate the solvent-co-solute behavior…
Despite the spontaneity of some in vitro protein folding reactions, native folding in vivo often requires the participation of barrel-shaped multimeric complexes known as chaperonins. Although it has long been known that chaperonin…
We introduce a simple theoretical approach for an equilibrium study of proteins with known native state structures. We test our approach with results on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and the alpha…
Physico-mechanical properties of polymers in solid state, in particular conditions of their structural transformations, are substantially defined by existence and mobility of elementary nonlinear excitations. The localized oscillatory…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…
We study inhomogeneous multidimensional cosmological models with a higher dimensional space-time manifold under dimensional reduction. Stability due to different types of effective potentials is analyzed for specific configurations of…
We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each…
We relate stability properties (i.e. moment exponents) of a stochastic dynamical system on a compact manifold $M$ to the homotopy and integral homology groups of $M$. In the special case of gradient Brownian systems associated to isometric…
Molecular dynamics (MD) simulations of crystalline poly(ethylene oxide) (PEO) have been carried out in order to study its vibrational properties. The vibrational density of states has been calculated using a normal mode analysis (NMA) and…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
We study dilute suspensions of magnetic nanoparticles in a nematic host, on two-dimensional (2D) polygons. These systems are described by a nematic order parameter and a spontaneous magnetization, in the absence of any external fields. We…
The emergence of spatially variable local dynamics, or dynamic heterogeneity, is common in multicomponent polymer systems. Although often attributed to differences in the intrinsic dynamics of each component, the molecular origin of their…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
Collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms, first by phosphorylation at, and second by reduction and oxidation of the Cys504…
It is shown that on compact hyperbolic manifolds, certain stable configurations of points which mutually repel along all interconnecting geodesics become equidistributed as the number of points increases
Liquid mixtures of many interacting components often exhibit numerous coexisting types of droplets. An exciting example is the cytosol of biological cells, where diverse droplets, called condensates, are essential for cellular function.…
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size…
To understand the mechanism of trimethylamine N-oxide (TMAO) induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (Leucine, L2, Serine, S2, Glutamine, Q2, Lysine, K2,…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…