Biomedical subjects

Roberto Car

Publications and source records attributed to Roberto Car.

27 records · Page 2Linked to original sources

PubMed2004

Current in open quantum systems.

We show that a dissipative current component is present in the dynamics generated by a Liouville-master equation, in addition to the usual component associated with Hamiltonian evolution. The dissipative component originates from coarse graining in time, implicit in a master equation, and needs to be included to preserve current continuity. We derive an explicit expression for the dissipative current in the context of the Markov approximation. Finally, we illustrate our approach with a simple numerical example, in which a quantum particle is coupled to a harmonic phonon bath and dissipation is described by the Pauli master equation.

Journal Article↗

PubMed2004

Mapping potential energy surfaces.

A recently proposed dynamical method [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002)] allows us to globally sample the free energy surface. This approach uses a coarse-grained non-Markovian dynamics to bias microscopic atomic trajectories. After a sufficiently long simulation time, the global free energy surface can be reconstructed from the non-Markovian dynamics. Here we apply this scheme to study the T=0 free energy surface, i.e., the potential energy surface in coarse-grained space. We show that the accuracy of the reconstructed potential energy surface can be dramatically improved by a simple postprocessing procedure with only minor computational overhead. We illustrate this approach by conducting conformational analysis on a small organic molecule, demonstrating its superiority over traditional unbiased approaches in sampling potential energy surfaces in coarse-grained space.

Journal Article↗

PubMed2004

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: spectral signatures of hydrogen bond breaking in liquid water.

We calculate the near-edge x-ray-absorption fine structure of H(2)O in the gas, hexagonal ice, and liquid phases using heuristic density-functional based methods. We present a detailed comparison of our results with experiment. The differences between the ice and water spectra can be rationalized in terms of the breaking of hydrogen bonds around the absorbing molecule. In particular the increase in the pre-edge absorption feature from ice to water is shown to be due to the breaking of a donor hydrogen bond. We also find that in water approximately 19% of hydrogen bonds are broken.

Journal Article↗

PubMed2003

Role of ligand bending in the photodissociation of O2 vs CO-heme: a time-dependent density functional study.

Time-dependent DFT calculations reveal a strong dependence of low-lying excited states on the <Fe-O-O angle of a model O2-heme adduct and ready access to a metastable side-on isomer. The predicted state crossings provide a pathway for internal conversion to the ground state and account for the low quantum yield for O2 dissociation, while the side-on isomer can account for the observation of an unphotolyzable fraction at low temperature. For CO-heme, the angle-sensitive states lie above the photoaccessed Q state and do not participate in photodissociation.

Carbon Monoxide↗

PubMed2003

Chemistry between magnesium and multiple molecules in tris(8-hydroxyquinoline) aluminum films.

Metal organic contacts are at the basis of devices such as organic light emitting diodes (OLEDs). Here, we report a theoretical investigation of the chemical interaction between a Mg atom and an organic film made of tris(8-hydroxyquinoline)aluminum (Alq3) molecules. The latter is modeled either by an isolated molecule or by a bulk crystal. Using first-principles molecular dynamics for structural optimization, we find that an isolated Alq3 molecule and a Mg atom form an ion-pair. However, when the metal atom interacts with molecules in a bulk crystalline environment, we find that an organometallic complex is energetically preferred over the ion-pair. The complex formation is an effect of the environment which makes possible the interaction of the metal atom with several adjacent molecules. Here, our calculated O(1s) and N(1s) core level shifts agree well with recent experimental data on Alq3 films exposed to Mg. Our results resolve the apparent contradiction between experiment and predictions made in previous calculations in which a single Alq3 molecule was used to model a thin film.

Journal Article↗

PubMed2003

Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules.

We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.

Adenine Nucleotides↗

PubMed2002

Pressure-induced structural changes in liquid SiO2 from Ab initio simulations.

First-principles molecular dynamics simulations at constant pressure have been used to investigate the mechanisms of compression of liquid SiO2. Liquid SiO2 is found to become denser than quartz at a pressure of about 6 GPa, in agreement with extrapolations of lower pressure experimental data. The high compressibility of the liquid is traced to medium-range changes in the topology of the atomic network. These changes consist in an increase of network connectivity caused by the pressure-induced appearance of coordination defects.

Journal Article↗

PubMed2002

Theory of quantum annealing of an Ising spin glass.

Probing the lowest energy configuration of a complex system by quantum annealing was recently found to be more effective than its classical, thermal counterpart. By comparing classical and quantum Monte Carlo annealing protocols on the two-dimensional random Ising model (a prototype spin glass), we confirm the superiority of quantum annealing relative to classical annealing. We also propose a theory of quantum annealing based on a cascade of Landau-Zener tunneling events. For both classical and quantum annealing, the residual energy after annealing is inversely proportional to a power of the logarithm of the annealing time, but the quantum case has a larger power that makes it faster.

Journal Article↗

PubMed2002

A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.

We used classical molecular mechanics (MM) simulations and quantum mechanical (QM) structural relaxations to examine the active site of myosin when bound to ATP. Two conformations of myosin have been determined by x-ray crystallography. In one, there is no direct interaction between switch 2 and the nucleotide (open state). In the other (closed state), the universally conserved switch 2 glycine forms a hydrogen bond with a gamma-phosphate oxygen. MM simulations indicate that the two states are thermodynamically stable and allow us to investigate the extent to which the P-loop, switch 1, and switch 2 are involved in hydrolysis. We find that the open structure has a higher affinity for ATP than the closed structure, and that ATP is distorted toward a transition state by interactions with the protein. We also examine how the structure of the binding site changes with either MgATP or CaATP as the nucleotide in myosin in the open conformer. Our analyses suggest that higher CaATPase rates occur because the leaving phosphate (P(i)) group is more weakly bound and dissociation occurs faster. Finally, we validate the use of a particular formulation of a QM methodology (Car-Parrinello) to further refine the structures of the active site.

Adenosine Triphosphate↗