Computational Studies of Molecular Mechanisms Mediating Protein Adsorption on Material Surfaces

Protein adsorption at material surfaces is a fundamental concept in many scientific applications ranging from the biocompatibility of implant materials in bioengineering to cleaning environmental material surfaces from toxic proteins in the area of biodefense. Understanding the molecular-level details of protein-surface interactions is crucial for controlling protein adsorption. While a range of experimental techniques has been developed to study protein adsorption, these techniques cannot produce the fundamental molecular-level information of protein adsorption. All-atom empirical force field molecular dynamics (MD) simulations hold great promise as a valuable tool for elucidating and predicting the mechanisms governing protein adsorption. However, current MD simulation methods have not been validated for this application. This research addresses three limitations of the standard MD when applied to the simulations of the protein-surface interactions: (1) representation of the force field parameters governing the interactions of protein amino acids with the material surface; (2) cluster analysis of ensembles of adsorbed protein states obtained in protein-adsorption simulations, in which in addition to the conformation the orientation of the sampled states is also important; and (3) simulation time to ensure a significant level of conformational sampling to cover the entire rough energy landscape of such a large molecular system as protein adsorption. This study, thus, attempted to further advance protein-adsorption simulation methods using high-density polyethylene as a model materials surface

Chern-Simons Correlations on (2+1)D Lattice

We have computed the contribution of zero modes to the value of the number of particles in the model of discrete (2+1)-dimensional nonlinear Schr\"odinger equation. It is shown for the first time that in the region of small values of the Chern-Simons coefficient k there exists a universal attraction between field configurations. For k=2 this phenomenon may be a dynamic origin of the semion pairing in high temperature superconducting state of planar systems.Comment: 9 pages, 2 figures Sabj-class: Strongly Correlated Electron

Saturable discrete vector solitons in one-dimensional photonic lattices

Localized vectorial modes, with equal frequencies and mutually orthogonal polarizations, are investigated both analytically and experimentally in a one-dimensional photonic lattice with saturable nonlinearity. It is shown that these modes may span over many lattice elements and that energy transfer among the two components is both phase and intensity dependent. The transverse electrically polarized mode exhibits a single-hump structure and spreads in cascades in saturation, while the transverse magnetically polarized mode exhibits splitting into a two-hump structure. Experimentally such discrete vector solitons are observed in lithium niobate lattices for both coherent and mutually incoherent excitations.Comment: 4 pages, 5 figures (reduced for arXiv

Stability of solitary waves for the generalized higher-order Boussinesq equation

This work studies the stability of solitary waves of a class of sixth-order Boussinesq equations.Comment: 32 pages. Submitte

System for Contributing and Discovering Derived Mission and Science Data

A system was developed to provide a new mechanism for members of the mission community to create and contribute new science data to the rest of the community. Mission tools have allowed members of the mission community to share first order data (data that is created by the mission s process in command and control of the spacecraft or the data that is captured by the craft itself, like images, science results, etc.). However, second and higher order data (data that is created after the fact by scientists and other members of the mission) was previously not widely disseminated, nor did it make its way into the mission planning process

From nonassociativity to solutions of the KP hierarchy

A recently observed relation between 'weakly nonassociative' algebras A (for which the associator (A,A^2,A) vanishes) and the KP hierarchy (with dependent variable in the middle nucleus A' of A) is recalled. For any such algebra there is a nonassociative hierarchy of ODEs, the solutions of which determine solutions of the KP hierarchy. In a special case, and with A' a matrix algebra, this becomes a matrix Riccati hierarchy which is easily solved. The matrix solution then leads to solutions of the scalar KP hierarchy. We discuss some classes of solutions obtained in this way.Comment: 7 pages, 4 figures, International Colloquium 'Integrable Systems and Quantum Symmetries', Prague, 15-17 June 200

Energy Bounds of Linked Vortex States

Energy bounds of knotted and linked vortex states in a charged two-component system are considered. It is shown that a set of local minima of free energy contains new classes of universality. When the mutual linking number of vector order parameter vortex lines is less than the Hopf invariant, these states have lower-lying energies.Comment: 4 pages, Latex2

An Extensible, User- Modifiable Framework for Planning Activities

This software provides a development framework that allows planning activities for the Mars Science Laboratory rover to be altered at any time, based on changes of the Activity Dictionary. The Activity Dictionary contains the definition of all activities that can be carried out by a particular asset (robotic or human). These definitions (and combinations of these definitions) are used by mission planners to give a daily plan of what a mission should do. During the development and course of the mission, the Activity Dictionary and actions that are going to be carried out will often be changed. Previously, such changes would require a change to the software and redeployment. Now, the Activity Dictionary authors are able to customize activity definitions, parameters, and resource usage without requiring redeployment. This software provides developers and end users the ability to modify the behavior of automatically generated activities using a script. This allows changes to the software behavior without incurring the burden of redeployment. This software is currently being used for the Mars Science Laboratory, and is in the process of being integrated into the LADEE (Lunar Atmosphere and Dust Environment Explorer) mission, as well as the International Space Station

Quantum vortices in systems obeying a generalized exclusion principle

The paper deals with a planar particle system obeying a generalized exclusion principle (EP) and governed, in the mean field approximation, by a nonlinear Schroedinger equation. We show that the EP involves a mathematically simple and physically transparent mechanism, which allows the genesis of quantum vortices in the system. We obtain in a closed form the shape of the vortices and investigate its main physical properties. PACS numbers: 03.65.-w, 03.65.Ge, 05.45.YvComment: 7 pages, 4 figure