相关论文: Role of anisotropy for protein-protein encounter
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
We compute the moments of the nonlinear binary collision integral in the ultrarelativistic hard-sphere approximation for an arbitrary anisotropic distribution function in the local rest frame. This anisotropic distribution function has an…
Understanding anomalous transport and reaction kinetics due to microscopic physical and chemical disorder is a long-standing goal in many fields including geophysics, biology, and engineering. We consider reaction-diffusion characterized by…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
The precipitate shape, size and distribution are crucial factors which determine the properties of several technologically important alloys. Elastic interactions between the inclusions modify their morphology and align them along…
Elliptic flow in ultrarelativistic heavy-ion collisions results from the hydrodynamic response to the spatial anisotropy of the initial density profile. A long-standing problem in the interpretation of flow data is that uncertainties in the…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
We present an event-driven molecular dynamics study for hard ellipses and assess the effects of aspect ratio and area fraction on their physical properties. For state points in the plane of aspect ratio (k=1-9) and area fraction…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
Microstructured particles are widely used in industries and state-of-the-art research and development. Diffusion of particles, particularly, controlled diffusion by a remotely applied field, has inspired novel applications ranging from…