This paper deals with solutions to the Vlasov-Poisson system with an infinite mass. The solution to the Poisson equation cannot be defined directly because the macroscopic density is constant at infinity. To solve this problem, we decompose the solution to the kinetic equation into a homogeneous function and a perturbation. We are then able to prove an existence result in short time for weak so...

We report measurements of the streaming current, an electrical current generated by a pressure-driven liquid flow, in individual rectangular silica nanochannels down to 70 nm in height. The streaming current is observed to be proportional to the pressure gradient and increases with the channel height. As a function of salt concentration, it is approximately constant below approximately 10 mM, w...

The molecular Gaussian surface has been frequently used in the field of molecular modeling and simulation. Typically, the Gaussian surface is defined using two controlling parameters; the decay rate and isovalue. Currently, there is a lack of studies in which a systematic approach in the determination of optimal parameterization according to the geometric features has been done. In this paper, ...

The use of molecular simulation to estimate the strength of macromolecular binding free energies is becoming increasingly widespread, with goals ranging from lead optimization and enrichment in drug discovery to personalizing or stratifying treatment regimes. In order to realize the potential of such approaches to predict new results, not merely to explain previous experimental findings, it is ...

We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation ...

A method, called beatification, is presented for rapidly extracting weakly nonlinear Hamiltonian systems that describe the dynamics near equilibria of systems possessing Hamiltonian form in terms of noncanonical Poisson brackets. The procedure applies to systems like fluids and plasmas in terms of Eulerian variables that have such noncanonical Poisson brackets, i.e., brackets with nonstandard a...

Effects of amyloid beta (Aβ) peptide Aβ(40) on secondary structures of Aβ(42) are studied by all-atom simulations using the GROMOS96 43a1 force field with explicit water. It is shown that in the presence of Aβ(40) the beta-content of monomer Aβ(42) is reduced. Since the fibril-prone conformation N∗ of full-length Aβ peptides has the shape of beta strand-loop-beta strand this result suggests tha...

The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and ...

Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explored mainly in academic settings due to the high computational requirements and s...

Cytarabine, daunorubicin, doxorubicin and vincristine are clinically used for combinatorial therapies of cancers in different combinations. However, the knowledge about the interaction of these drugs with the metabolizing enzyme cytochrome P450 is limited. Therefore, we utilized computational methods to predict and assess the drug-binding modes. In this study, we performed docking, MD simulatio...