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A prophylactic or therapeutic vaccine offers the best hope to curb the HIV-AIDS epidemic gripping sub-Saharan Africa, but it remains elusive. A major challenge is the extreme viral sequence variability among strains. Systematic means to guide immunogen design for highly variable pathogens like HIV are not available. Using computational models, we have(More)
Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design. To address this challenge, our group has developed a computational model, rooted in physics, that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness, thus blocking viable escape routes. Here,(More)
Molecular simulation is an important and ubiquitous tool in the study of microscopic phenomena in fields as diverse as materials science, protein folding and drug design. While the atomic-level resolution provides unparalleled detail, it can be non-trivial to extract the important motions underlying simulations of complex systems containing many degrees of(More)
We present a systematic study of the photophysical properties of one-dimensional electronically delocalized nanostructures assembled from π-conjugated subunits embedded within oligopeptide backbones. The nature of the excited states within these nanostructures is studied as a function of primary amino acid sequence utilizing steady-state and time-resolved(More)
Nanomedicines (NMs) offer new solutions for cancer diagnosis and therapy. However, extension of progression-free interval and overall survival time achieved by Food and Drug Administration-approved NMs remain modest. To develop next generation NMs to achieve superior anticancer activities, it is crucial to investigate and understand the correlation between(More)
The antimicrobial peptide microcin J25 (MccJ25) is posttranslationally matured from a linear preprotein into its native lasso conformation by two enzymes. One of these enzymes cleaves the preprotein and the second enzyme installs the requisite isopeptide bond to establish the lasso structure. Analysis of a mimic of MccJ25 that can be cyclized without the(More)
We employ the diffusion map approach as a nonlinear dimensionality reduction technique to extract a dynamically relevant, low-dimensional description of n-alkane chains in the ideal-gas phase and in aqueous solution. In the case of C8 we find the dynamics to be governed by torsional motions. For C16 and C24 we extract three global order parameters with(More)
Bottom-up self-assembly offers a means to synthesize materials with desirable structural and functional properties that cannot easily be fabricated by other techniques. An improved understanding of the structural pathways and mechanisms by which self-assembling materials spontaneously form from their constituent building blocks is of value in understanding(More)
Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamical motions of the system. For molecular systems exhibiting free energy barriers exceeding a few k(B)T, inadequate sampling of the barrier regions between stable(More)
We employ molecular dynamics simulations to study the solubility and molecular conformations of n-alkane chains in water. We find nearly exponential decrease in solubility with carbon number up to n-eicosane (C(20)), and excellent agreement with experiment up to n-dodecane (C(12)). We detect no sharp break in the dependence of the solubility upon carbon(More)