A5065904104- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Advanced biosensing and bioanalysis techniques
- Dynamics and Control of Mechanical Systems
- Elasticity and Material Modeling
- Genomics and Chromatin Dynamics
- Numerical methods for differential equations
- Control and Dynamics of Mobile Robots
- Bacteriophages and microbial interactions
- Geometric and Algebraic Topology
- Robotic Path Planning Algorithms
- Nonlinear Waves and Solitons
- Taxation and Legal Issues
- Adhesion, Friction, and Surface Interactions
- Quantum chaos and dynamical systems
- Force Microscopy Techniques and Applications
- Cooperative Studies and Economics
- Robotic Mechanisms and Dynamics
- Advanced Materials and Mechanics
- Advanced Numerical Methods in Computational Mathematics
- Financial Reporting and Valuation Research
- RNA Research and Splicing
- Diffusion and Search Dynamics
- Elasticity and Wave Propagation
Duke University Health System
2025
École Polytechnique Fédérale de Lausanne
2014-2024
Rutgers, The State University of New Jersey
2009-2023
Universidad de Navarra
2012
Universitat Politècnica de València
2012
Institute of Public Finance
2012
Université Claude Bernard Lyon 1
2009
Centre National de la Recherche Scientifique
2009
Universitat Politècnica de Catalunya
2009
Tulane University
2009
We describe Curves+, a new nucleic acid conformational analysis program which is applicable to wide range of structures, including those with up four strands and either canonical or modified bases backbones. The algorithmically simpler computationally much faster than the earlier Curves approach, although it still provides both helical backbone parameters, curvilinear axis parameters relating position this axis. It additionally full groove widths depths. Curves+ can also be used analyse...
It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays role in protein–DNA interactions vital for cellular processes. Understanding predicting effects requires an extensive structural dynamic dataset which currently unavailable from experiment. A consortium laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing not only all 10 unique pair steps, but also possible...
We present the results of microsecond molecular dynamics simulations carried out by ABC group laboratories on a set B-DNA oligomers containing 136 distinct tetranucleotide base sequences. demonstrate that resulting trajectories have extensively sampled conformational space accessible to at room temperature. confirm sequence effects depend strongly not only specific pair step, but also pairs flank each step. Beyond average helical parameters and fluctuations, we identify sequences oscillate...
The global radius of curvature a space curve is introduced. This function related to, but distinct from, the standard local and connected to various physically appealing properties curve. In particular, provides concise characterization thickness curve, certain ideal shapes knots as have been investigated within context DNA.
A wheeled mobile robot is here modelled as a planar rigid body that rides on an arbitrary number of wheels. The rela tionship between the motion and steering drive rates wheels developed. In particular, conditions are obtained guarantee rolling without skidding or sliding can occur. Explicit differential equations derived to describe motions arise in such ideal trajectories. simplest wheel configura tion permits access rigid-body determined. Then question slippage due misalign ment...
Abstract We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by data derived from molecular dynamics simulations. The analysis is based on use of curvilinear helicoidal coordinates leads to highly localized ion densities compared those obtained simply superposing snapshots in Cartesian space. results identify populated sequence-dependent regions where ions strongly interact with are coupled its conformational...
Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform detailed analysis how potassium ions interact the double helix. The studied contain all 136 distinct tetranucleotides and we are thus able make comprehensive base sequence effects. Using recently developed curvilinear helicoidal coordinate method analyze details ion populations densities within major minor grooves space surrounding...
A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used predict a sequence-averaged persistence length lF = 53.5 nm in sense Flory, and lp 160 bp or apparent tangent-tangent correlation decay. These estimates are slightly higher than consensus experimental values 150 50 nm, but we believe agreement be good given that itself parametrized from molecular dynamics simulations short fragments 10-20 bp, with no explicit fit length. Our further...
Importance The rise of patient messages sent to clinicians via a portal has directly led physician burnout and dissatisfaction, prompting uptake artificial intelligence (AI) alleviate this burden. It is important understand preferences around AI in patient-clinician communication as ethical guidelines on appropriate use disclosure (patient notification use) are developed. Objective To analyze regarding electronic messages. Design, Setting, Participants A survey study was conducted within the...
Experimentally motivated parameters from a base-pair-level discrete DNA model are averaged to yield for continuum elastic rod with curved unstressed shape reflecting the local geometry. The permits computations discretization lengths longer than intrinsic of base-pair model, and, this and other reasons, yields an efficient computational formulation. Obtaining stiffnesses is straightforward, but obtaining hindered by ‘‘noisy’’ small-scale structure rapid helix twist shape. Filtering data...
Helices are among the simplest shapes that observed in filamentary and molecular structures of nature. The local mechanical properties such often modeled by a uniform elastic potential energy dependent on bending twist, which is what we term rod model. Our first result to complete semi-inverse classification, initiated Kirchhoff, all infinite, helical equilibria inextensible, unshearable rods with energies general quadratic function flexures twist. Specifically, demonstrate can be found...
Guanine, one of the four DNA bases, has been observed by tunneling microscopy to form a two-dimensional ordered structure on two crystalline substrates, graphite and MoS2. The lattice formed guanine is nearly identical surfaces, heteroepitaxy appears be growth mechanism in both cases. Although resolution molecular details superior for substrate, simpler results MoS2 are not only easier interpret but also facilitate understanding more complex images graphite. We propose that interfacial...
Abstract We consider the stability of multi‐ or n ‐soliton solutions to Korteweg‐de Vries equation (KdV) posed on real line. It is shown that in standard variational characterization KdV multi‐solitons as critical points, ‐solitons actually realize non‐isolated constrained minimizers. (The case = 1 was already known Benjamin; see [6].) From this fact a precise dynamic result for follows, namely, initial data close given evolves time so remain (in H (𝔑) Sobolev norm) ‐dimensional manifold all...
Abstract Given two samples of continuous zero-mean iid Gaussian processes on [0,1], we consider the problem testing whether they share same covariance structure. Our study is motivated by determining mechanical properties short strands DNA are significantly affected their base-pair sequence; though expected to be true, had so far not been observed in three-dimensional electron microscopy data. The seen involve aspects ill-posed inverse problems and a test based Karhunen–Loève approximation...
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing large amount atomistic molecular dynamics simulations, we determine sequence-dependent DNA as expressed in equilibrium distribution its stochastic dynamics. Our analysis includes study first second moments distribution, which can be accurately captured by harmonic model, but with nonlocal sequence-dependence. characterize choreography backbone...
A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models DNA in solution from atomistic molecular dynamics simulations. The properly consistent with equilibrium statistical mechanics, leads effective shape, stiffness mass parameters, employs special procedures treating spontaneous torsion angle flips H-bond breaks, both which can have significant effect on the results. accompanied by various analytical consistency checks...
A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models B-form DNA in solution is introduced. The depends on both the assumed range energetic couplings, and extent sequence dependence model parameters. significant feature that they exhibit phenomenon frustration: each base cannot simultaneously minimize energy all its interactions. As a consequence, an arbitrary oligomer has intrinsic or pre-existing stress, with level this frustration dependent particular oligomer....