Related papers: The dynamics of viruslike capsid assembly and disa…
We study the depletion-induced self-assembly of indented colloids. Using state-of-the-art Monte Carlo simulation techniques that treat the depletant particles explicitly, we demonstrate that colloids assemble by a lock-and-key mechanism,…
We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation…
A simple model is proposed aimed to investigate how the amount of dissociated ions influences the mechanical stability of viral capsids. After an osmotic and mechanical equilibrium is established with the outer solution, a non-adiabatic…
Viral infectious diseases, such as HIV virus growth, cause an important health concern. Study of intracellular viral processes can provide us to develop drug and understanding the drug dose to decrease the HIV virus in during growth.…
Most spherical viruses exhibit icosahedral symmetry, yet the growth of viral shells remains poorly understood due to the short lifetimes and broad size distribution of assembly intermediates. Classical nucleation theory has been widely…
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials…
The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach,…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
An extended polymer collapses to form a globule when subjected to a quench below the collapse transition temperature. The process begins with the formation of clusters of monomers or ``pearls''. The nascent clusters merge, resulting in…
Wormlike micelles are self-assemblies of polymer chains that can break and recombine reversibly. In this paper, we derive a thermodynamically consistent two species micro-macro model of wormlike micellar solutions by employing an energetic…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
We develop a comprehensive theoretical biophysics model grounded in a path integral perspective and an m-sectorial open-system framework, to describe complex, damped viral phonon dynamics in resource limited and noise driven environments.…
Applying constant tensile stress to a piece of amorphous solid results in a slow extension, followed by an eventual rapid mechanical collapse. This "creep" process is of paramount engineering concern, and as such was the subject of study in…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
While providing a highly accurate framework for simulating laser-induced many-electron dynamics in atom and molecules, including linear and nonlinear steady-state and transient absorption spectra, time-dependent coupled-cluster theory does…
Aggregation of chemotactic bacteria under a unimodal distribution of chemical cues was investigated by Monte Carlo (MC) simulation based on a kinetic transport equation, which considers an internal adaptation dynamics as well as a finite…
We investigate the structural and topological properties of hydrophobic homopolymer chains in aqueous solutions using molecular dynamics simulations and circuit topology (CT) analysis. By combining geometric observables, such as radius of…
Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work,…