Interrupted coarse-grained theory of quasi-conitinuum photoexcitation

We propose a theory of quasi-continuum phenomena in unimolecular photoreactions. The theory is simple enough not to require computer implementation but is able to reproduce analytically and semi-quantitatively the results of full computer simulations.     

Free energies of molecular crystal surfaces by computer simulation: application to tetrathiophene

We describe a general simulation protocol for the evaluation of the surface free energies of molecular crystals, which are of broad interest for phenomena such as polymorphism and crystal growth. The method has been applied to selected surfaces of two polymorphs of tetrathiophene. The simulations highlight an important temperature-dependent entropic contribution to the surface free energies, which is not included in widely used static simulations of surface structure and energetics.     

Coulombic dragging of molecules on surfaces induced by separately flowing liquids

We demonstrate that ions or polar molecules can be driven by fluctuating Coulombic forces induced by flowing polar liquids at nanometer separations. We simulate this intriguing phenomenon on small ions and polar molecules driven on the surfaces of carbon nanotubes through which a flow of water is passing. Our simulations show that the average velocities of the driven molecules are close to those of the passing liquid. These transport phenomena open the door for many potential applications.     

Molecular simulations of solute transport in xylose isomerase crystals

Cross-linked enzyme crystals (CLECs) enclose an extensive regular matrix of chiral solvent-filled nanopores, via which ions and solutes travel in and out. Several cross-linked enzyme crystals have recently been used for chiral separation and as biocatalysts. We studied the dynamics of solute transport in orthorhombic d-xylose isomerase (XI) crystals by means of Brownian dynamics (BD) and molecular dynamics (MD) simulations, which show how the protein residues influence the dynamics of solute molecules in confined regions inside the lattice. In the BD simulations, coarse-grained beads represent solutes of different sizes. The diffusion of S-phenylglycine molecules inside XI crystals is investigated by long-time MD simulations. The computed diffusion coefficients within a crystal are found to be orders of magnitude lower than in bulk water. The simulation results are compared to the recent experimental studies of diffusion and reaction inside XI crystals. The insights obtained from simulations allow us to understand the nature of solute-protein interactions and transport phenomena in CLECs, which is useful for the design of novel nanoporous biocatalysts and bioseparations based on CLECs.     

Molecular simulation of condensation process of Lennard-Jones fluids confined in nanospace with jungle-gym structure

We report grand canonical Monte Carlo simulations for a Lennard-Jones (LJ) fluid modeled on methane confined in nanospace with jungle-gym-like (JG) cubic structure, which is typically found in porous coordination polymers. Pillars composing the cubic structure were modeled as structureless smooth solid rods made of LJ carbon. We examined the effects of pore size, pore geometry, rod thickness, and rod potential onto the condensation phenomena in the JG pore structure. The simulations clarified that the condensation pressure and adsorption amount in the JG structure were influenced by pore size and rod potential, while the transition type was determined by rod thickness. The characteristics of the JG structure lie in the sensitivity to the slight changes in pore size, rod thickness, and rod potential owing to the combination of the packing effect of molecules and the superposition effect of rod potentials.     

Antiplasticization and local elastic constants in trehalose and glycerol mixtures

We have performed molecular dynamics simulations of glassy trehalose with various amounts of glycerol in order to explore the tendency for glycerol to antiplasticize the glass. We find that below a temperature of 300 K, the average density of the system containing 5%(wt) glycerol is larger than that of the pure trehalose system; the glass transition temperature is decreased, and the elastic constants are essentially unchanged. Taken together, these phenomena are indicative of mild antiplasticization, a type of behavior generally observed in polymeric systems. We have calculated the local elastic constants in our glassy materials and, consistent with previous simulations on a coarse-grained polymer, we find evidence of domains having negative elastic moduli. We have explored the ability of various measures of the Debye-Waller factor u(2) to predict the stiffness of our systems in terms of their elastic constants. We find that u(2) is indeed correlated with the behavior of the bulk elastic constants. On a local level, a correlation exists between the local moduli and u(2); however, that correlation is not strong enough to arrive at conclusive statements about the local elastic properties.     

Study on Non-Newtonian Behaviors of Lennard-Jones Fluids via Molecular Dynamics Simulations

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheological behaviors of a monoatomic fluid governed by the Lennard-Jones potential. Both steady Couette and oscillatory shear flows are investigated. Shear thinning and normal stress effects are observed in the steady Couette flow simulations. The radial distribution function is calculated at different shear rates to exhibit the change of the microscopic structure of molecules due to shear. We observe that for a larger shear rate the repulsion between molecules is more powerful while the attraction is weaker, and the above phenomena can also be confirmed by the analyses of the potential energy. By applying an oscillatory shear to the system, several findings are worth mentioning here:First, the phase difference between the shear stress and shear rate increases with the frequency. Second, the real part of complex viscosity first increases and then decreases while the imaginary part tends to increase monotonically, which results in the increase of the proportion of the imaginary part to the real part with the increasing frequency. Third, the ratio of the elastic modulus to the viscous modulus also increases with the frequency. These phenomena all indicate the appearance of viscoelasticity and the domination of elasticity over viscosity at high oscillation frequency for Lennard-Jones fluids.     

Simulations of self-assembling systems

The previous focus on the thermodynamics of self-assembly of surfactants in solution through simulations is now being expanded to include phenomena in the fluid dynamic regime. This expansion implies that a formal edifice must be built to link molecular dynamics smoothly to mesoscopic and macroscopic length and time scales. We summarize and comment on recent trends in this area along with new results based on classical approaches. The latter include molecular dynamics as well as off-lattice Monte Carlo simulations and lattice-based Guggenheim-type models.     

Rigid quantum Monte Carlo simulations of condensed molecular matter: water clusters in the n=2-->8 range

The numerical advantage of quantum Monte Carlo simulations of rigid bodies relative to the flexible simulations is investigated for some simple systems. The results show that if high frequency modes in molecular condensed matter are predominantly in the ground state, the convergence of path integral simulations becomes nonuniform. Rigid body quantum parallel tempering simulations are necessary to accurately capture thermodynamic phenomena in the temperature range where the dynamics are influenced by intermolecular degrees of freedom; the stereographic projection path integral adapted for quantum simulations of asymmetric tops is a significantly more efficient strategy compared with Cartesian coordinate simulations for molecular condensed matter under these conditions. The reweighted random series approach for stereographic path integral Monte Carlo is refined and implemented for the quantum simulation of water clusters treated as an assembly of rigid asymmetric tops.     

Molecular simulation of binary colloidal mixtures: Gelation and aging phenomena

We investigate the aging dynamics of colloidal depletion gel by computer simulation. In this study, we employ an alternative approach using the effective pair potential to avoid the slow convergence in binary mixtures due to cage effect, and the structural formation of colloidal depletion gels is then clarified. We study the mean square displacement (MSD) of each segment in depletion gels by stochastic molecular dynamic simulations. It is shown that the MSD obeys a power-law, indicating sub-diffusive behavior of depletion gels. We also observe aging phenomena of the colloidal depletion gels from intermediate scattering functions. Power-law behavior of a characteristic time in this system, as a function of a waiting time, is also clarified.     

Statistical evaluation of single nano-object fluorescence.

Single nano-objects display strong fluctuations of their fluorescence signals. These random and irreproducible variations must be subject to statistical analysis to provide microscopic information. We review the main evaluation methods used so far by experimentalists in the field of single-molecule spectroscopy: time traces, correlation functions, distributions of "on" and "off" times, higher-order correlations. We compare their advantages and weaknesses from a theoretical point of view, illustrating our main conclusions with simple numerical simulations. We then review experiments on different types of single nano-objects, the phenomena which are observed and the statistical analyses applied to them.     

Zeta potential determination by streaming current modelization and measurement in electrophoretic microfluidic systems

Electrophoresis in capillary and microfluidic systems, used in analytical chemistry to separate charged species, are quite sensitive to surface phenomena in terms of separation performances. In order to improve theses performances, new surface functionalization techniques are required. There is a need for methods to provide fast and accurate quantification about surface charges at liquid/solid interfaces. We present a fast, simple, and low-cost technique for the measurement of the zeta-potential, via the modelization and the measurement of streaming currents. Due to the small channel cross section in microfluidic devices, the streaming current modelization is easier than the streaming potential measurement. The modelization combines microfluidic simulations based on the Navier-Stokes equation and charge repartition simulations based on the Poisson-Boltzmann equation. This method has been validated with square and circular cross section shape fused-silica capillaries and can be easily transposed to any lab-on-chip microsystems.     

Formation of stacking defects at surfaces: From atomistic simulations to density functional theory calculations

We have performed electronic structure calculations to study the evolution of the stacking fault energy at (111) surfaces of metals. We first apply an sp–d tight-binding model and then increase the accuracy on the electronic structure by using density functional theory (DFT) calculations. We show in this way the relative importance of sp–d hybridization both in the formation of defects at the surface of metals and in reconstruction phenomena as a function of band filling especially at the end of transition metal series. Comparing our results with atomistic simulations it is concluded that although atomistic calculations are powerful tools to investigate relaxation mechanisms at surfaces, a higher degree of accuracy on electronic structure is necessary to quantify the energy of some defects at surfaces like stacking faults. In particular long range interactions associated to less localized sp electrons are playing a rather important role in reconstruction phenomena for metals like platinum and gold. These results are backed up by DFT calculations applied to iridium, platinum and gold (111) surfaces.     

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

A method for performing implicit-solvent molecular dynamics simulations at constant pH was applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. As a reference, molecular dynamics simulations were done for the same peptide with two variants of its fixed protonation patterns expected to dominate at pH 4, i.e., with a protonated and a deprotonated side chain of the Asp residue and the protonated Lys residue in both cases. The dynamic trajectories of the peptide were used to discuss the problem of the significance of the solute-solvent proton exchange phenomena for the dynamics and structural distributions of the polypeptide chain. The Asp-Lys distance was used as a probe of the overall molecular structure of the investigated pentapeptide. To characterize the dynamics, distributions of the "waiting" times for a transition from a "short" distance conformation to a "long" distance conformation were constructed, based on the generated molecular dynamics trajectories. We show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule, although the average protonation probability of the short-distance conformation is close to zero. However, the distribution of the Asp-Lys distances obtained from constant-pH simulations cannot be reproduced as a linear combination of the distributions resulting from the simulations with fixed protonation states.     

Photoelectron spectroscopy of 1-nitropropane and 1-nitrobutane anions

We present low-energy velocity map photoelectron imaging results for bare and Ar-solvated 1-nitropropane and 1-nitrobutane anions. We report the adiabatic electron affinity of 1-nitropropane as (223 ± 6) meV and that of 1-nitrobutane as (240 ± 6 meV). The vertical detachment energies of these two species are found to be (0.92 ± 0.05) and (0.88 ± 0.05) eV, respectively. The photoelectron spectra are discussed in the framework of Franck-Condon simulations based on density functional theory. We observe unusual resonances in the photoelectron spectra of both ions under study, whose kinetic energy is independent of the photon energy of the detaching radiation. We discuss possible origins of these resonances as rescattering phenomena, consistent with the experimental photoelectron angular distributions.     

Nonadiabatic excited-state dynamics of polar pi-systems and related model compounds of biological relevance

Multireference ab initio dynamics simulations have become available as a tool for the investigation of photochemical processes, mainly for those related to nonadiabatic phenomena taking place in the sub-picosecond time scale. For organic molecules, these phenomena are in many cases deeply dependent on the relaxation of the photoexcited pi-system. We review the latest contributions of our group to this subject and report new results for systems studied previously, grouping them in single pi bonds, chains and aromatic rings. The dynamics of ethylene and substituted ethylenes is discussed mainly in connection to the competition between the two available relaxation paths in the excited states and their relation to the conical intersections in large systems. The trans-cis and the cis-trans dynamics of the pentadieniminium cation is investigated as well. Finally, we discuss the photodynamics of aminopyrimidine starting in the S1 and S2 states and the conclusions, which can be drawn from this for the interpretation of the adenine dynamics.     

Optimal control of ultrafast laser driven many-electron dynamics in a polyatomic molecule: N-methyl-6-quinolone

We report time-dependent configuration interaction singles calculations for the ultrafast laser driven many-electron dynamics in a polyatomic molecule, N-methyl-6-quinolone. We employ optimal control theory to achieve a nearly state-selective excitation from the S(0) to the S(1) state, on a time scale of a few ( approximately 6) femtoseconds. The optimal control scheme is shown to correct for effects opposing a state-selective transition, such as multiphoton transitions and other, nonlinear phenomena, which are induced by the ultrashort and intense laser fields. In contrast, simple two-level pi pulses are not effective in state-selective excitations when very short pulses are used. Also, the dependence of multiphoton and nonlinear effects on the number of states included in the dynamical simulations is investigated.     

Molecular dynamics study of the temperature-dependent Optical Kerr effect spectra and intermolecular dynamics of room temperature ionic liquid 1-methoxyethylpyridinium dicyanoamide

We have performed classical molecular dynamics simulations to calculate the Optical Kerr effect (OKE) spectra of 1-methoxyethylpyridinium dicyanoamide, a room-temperature ionic liquid (IL) which has been recently studied by Shirota and Castner (Shirota, H. ; Castner, E. J. Phys. Chem. A 2005, 109, 9388-9392) in comparison to its neutral isoelectronic solvent mixture. Our theoretical and computational studies show that the decay of the collective polarizability anisotropy correlation exhibits several different time scales originating from inter- and intramolecular dynamics, in good agreement with experiments. What's more, we find that the portion of the collective anisotropic polarizability relaxation due to "interaction-induced" phenomena is important at times much longer than those observed in normal solvents when these are far from their glass transition temperature. From our long (60 ns) molecular dynamics simulations, we are able to determine the appropriate time scales for orientational relaxation and interaction-induced processes occurring in the liquid. We find that the cationic contribution to the OKE signal is predominant. Because of the slow nature of relaxation processes in ILs, these calculations are very time, memory, and storage intensive. In the context of this research, we have developed a polarizable force field for this system and also theoretical methodology to generate molecular polarizabilities for arbitrarily shaped molecules and ions from corresponding atomic polarizabilities. We expect this methodology to have an important impact on the speed of molecular dynamics simulations of polarizable systems in the future.     

Dynamical fluctuation effects in glassy colloidal suspensions

Fundamental understanding of heterogeneous dynamics in concentrated glassy hard sphere fluids and colloidal suspensions, even at the single particle level, requires major theoretical advances. Recent simulations and confocal microscopy experiments suggest strong nongaussian dynamical fluctuation effects and activated transport emerge well before an apparent kinetic glass transition is reached. New theoretical approaches that can predict the observable signatures of intermittent large amplitude motions and the associated fluctuation phenomena are discussed. Comparisons are made with experiments, computer simulations, and prior theory for average dynamical properties.