Biomedical subjects

Christopher Roland

Publications and source records attributed to Christopher Roland.

8 recordsLinked to original sources

PubMed2006

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections.

There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe "rare events" and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)(2)-Pro-(Gly)(3)-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code.

Algorithms↗

PubMed2006

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations.

The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.

Computational Biology↗

PubMed2005

Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues.

The recent rise of vancomycin-resistant enterococci (VRE) and vancomycin-resistant Staphylococcus aureus (VRSA) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides, Ac-d-Ala-X, where X = d-Lac and d-Ser (characteristic of VREs) and X = d-Ala, Gly (characteristic of non-VREs), and a model "methylated d-Ala" CH(2)CH(CH(3))COO(-), in liquid as well as gas phase. The gas-phase ordering of the binding, from strongest to weakest, is Gly, d-Ala, d-Ser, CH(2)CH(CH(3))COO(-), and d-Lac. Calculations show that the order of the Gly and d-Ala binding is reversed in solution. The results are in good agreement with recent experimental findings.

Anti-Bacterial Agents↗

PubMed2005

Self-assembled patterns and strain-induced instabilities for modulated systems.

The self-assembled domain patterns of modulated systems are characteristic of a wide variety of chemical and physical systems, and are the result of competing interactions. From a technological point of view, there is considerable interest in these domain patterns, as they form suitable templates for the fabrication of nanostructures. We have analyzed the domains and instabilities that form in modulated systems, and show that a large variety of patterns--based on long-lived metastable or glassy states--may be formed as a compromise between the required equilibrium modulation period and the strain present in the system. The strain results from topologically constrained trajectories in phase space, that effectively preclude the equilibrium configuration.

Journal Article↗

PubMed2005

New and exotic self-organized patterns for modulated nanoscale systems.

The self-assembled domain patterns of modulated systems are the result of competing short-range attractive and long-range repulsive interactions found in diverse physical and chemical systems. From an application point of view, there is considerable interest in these domain patterns, as they form templates suitable for the fabrication of nanostructures. In this work we have generated a variety of new and exotic patterns, which represent either metastable or glassy states. These patterns arise as a compromise between the required equilibrium modulation period and the strain resulting from topologically constrained trajectories in phase space that effectively preclude the equilibrium configuration.

Computer Simulation↗

PubMed2004

First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini.

The recent rise of vancomycin-resistant enterococci (VRE) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin and teicoplanin with d-Ala-d-Lac (characteristic of VREs) and d-Ala-d-Ala (characteristic of non-VREs). Binding of both antibiotics to d-Ala-d-Ala was found to be stronger by about 3-5 kcal/mol and due primarily to the oxygen-oxygen lone-pair repulsion characteristic of the antibiotic/d-Ala-d-Lac complex. These results are in good agreement with recent experimental findings.

Alanine↗

PubMed2004

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations.

It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.

Algorithms↗

PubMed2002

Ab initio investigations of lithium diffusion in carbon nanotube systems.

Li-nanotube systems can substantially improve the capacity of Li-ion batteries by utilizing both nanotube exteriors and interiors. Our ab initio simulations show that while Li motion through the sidewalls is forbidden, Li ions can enter tubes through topological defects containing at least nine-sided rings, or through the ends of open-ended nanotubes. Once inside, their motion is not diffusion limited. These results suggest that "damaging" nanotube ropes by either chemical or mechanical means will yield superior material for electrochemical storage.

Journal Article↗