Biomedical subjects

David Reguera

Publications and source records attributed to David Reguera.

9 recordsLinked to original sources

PubMed2006

Finite-size effects in simulations of nucleation.

We investigate the importance of finite-size effects in simulations of nucleation processes. Most molecular dynamics simulations of first order phase transitions, such as vapor-liquid nucleation, are performed in the canonical NVT ensemble where, owing to the fixed total number of molecules N, the growth of the new phase causes the depletion of the metastable phase. This effect may lead to significant errors in the simulation and even to the impossibility of observing nucleation in a small finite system. We present a theory to estimate the system size beyond which these finite-size effects are expected to be negligible. This optimization saves valuable calculation time and can extend the range of supersaturations and rates attainable by simulations by several orders of magnitude. Our results are applicable to diverse situations, such as crystallization, capillary condensation, or the melting of nanoclusters.

Journal Article↗

PubMed2006

Classical line shapes based on analytical solutions of bimolecular trajectories in collision induced emission.

The classical theory of collision induced emission (CIE) from pairs of dissimilar atoms is studied. This radiation emitted by accelerating dipoles is produced essentially by their overlap and exchange interaction at short range. This classical calculation is based on exact collinear solutions of the trajectories of two spherical particles in a head-on collision under the influence of a Morse potential with a well of arbitrary depth. Without too restrictive conditions a variety of simple solutions in closed form is obtained that illustrates the connection between collision dynamics and CIE. Depending on the well depth and energy of the particles, they may radiate in the far infrared to infrared or visible and shorter wavelength regions. The results are characterized by a fixed total energy. Nevertheless, a connection is demonstrated between the line shape in CIE computed through the trajectory and that based on the emission of a thermally equilibrated system.

Energy Transfer↗

PubMed2006

Nucleation rates in a new phenomenological model.

In this paper we develop a new theory to evaluate the nucleation rate in the framework of the EMLD-DNT model. Beyond the model, our theory deals with cluster translation and exclusion, effects that have been virtually ignored in classical nucleation theory. We apply the model to the case of 1-pentanol, and compare the predictions with experimental results. We find an excellent agreement between the nucleation rate predicted by our theory and experimental data. The distinguishing feature of the model is its ability to predict successfully the rate of formation of the critical nucleus without the use of an intermolecular potential, employing only macroscopic thermodynamic properties.

Crystallization↗

PubMed2005

Classical nucleation theory of virus capsids.

A fundamental step in the replication of a viral particle is the self-assembly of its rigid shell (capsid) from its constituent proteins. Capsids play a vital role in genome replication and intercellular movement of viruses, and as such, understanding viral assembly has great potential in the development of new antiviral therapies and a systematic treatment of viral infection. In this article, we assume that nucleation is the underlying mechanism for self-assembly and combine the theoretical methods of the physics of equilibrium polymerization with those of the classical nucleation to develop a theory for the kinetics of virus self-assembly. We find expressions for the size of the critical capsid, the lag time, and the steady-state nucleation rate of capsids, and how they depend on both protein concentration and binding energy. The latter is a function of the acidity of the solution, the ionic strength, and the temperature, explaining why capsid nucleation is a sensitive function of the ambient conditions.

Binding Sites↗

PubMed2005

Mechanical properties of viral capsids.

Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres . In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the inhomogeneity of the shells that is inherent to their discrete and polyhedral nature. We calculate the distribution of stress in these capsids and analyze their response to isotropic internal pressure (arising, for instance, from genome confinement and/or osmotic activity). We compare our results with appropriate generalizations of classical (i.e., continuum) elasticity theory. We also examine competing mechanisms for viral shell failure, e.g., in-plane crack formation vs radial bursting. The biological consequences of the special stabilities and stress distributions of viral capsids are also discussed.

Biomechanical Phenomena↗

PubMed2004

Origin of icosahedral symmetry in viruses.

With few exceptions, the shells (capsids) of sphere-like viruses have the symmetry of an icosahedron and are composed of coat proteins (subunits) assembled in special motifs, the T-number structures. Although the synthesis of artificial protein cages is a rapidly developing area of materials science, the design criteria for self-assembled shells that can reproduce the remarkable properties of viral capsids are only beginning to be understood. We present here a minimal model for equilibrium capsid structure, introducing an explicit interaction between protein multimers (capsomers). Using Monte Carlo simulation we show that the model reproduces the main structures of viruses in vivo (T-number icosahedra) and important nonicosahedral structures (with octahedral and cubic symmetry) observed in vitro. Our model can also predict capsid strength and shed light on genome release mechanisms.

Biophysical Phenomena↗

PubMed2004

The role of fluctuations in both density functional and field theory of nanosystems.

The role of fluctuations in both the density functional theory (DFT) and the field theory (FT) of nanosystems is studied. It turns out that although fluctuations are rigorously incorporated into the general formalism of DFT, they are often omitted in the choice of an approximate free energy functional that must be constructed in order to solve the basic integral equation appearing in DFT. Aside from the analytical discussion, it is demonstrated, in connection with a particular system (fluid in a nanopore) that the effects of fluctuation are missing when one of the most common functionals for this system is used. The demonstration involves a comparison of the results of Monte Carlo simulation with the predictions of DFT when this free energy functional is used. The applicability of FT and DFT in the context of the theory of nucleation is also discussed.

Journal Article↗

PubMed2003

What drives the translocation of stiff chains?

We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian molecular dynamics simulations we investigate the mean first-passage time as a function of the length of the chain inside for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process that is in general quite different from that of a Brownian ratchet. Furthermore, nonequilibrium effects contribute significantly to the dynamics; e.g., the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value.

Binding Sites↗

PubMed2003

Viral self-assembly as a thermodynamic process.

The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal "switching" configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins.

Capsid↗