Biomedical subjects

Laurence E Fried

Publications and source records attributed to Laurence E Fried.

11 recordsLinked to original sources

PubMed2006

First principles simulation of a superionic phase of hydrogen fluoride (HF) at high pressures and temperatures.

We have conducted ab initio molecular dynamics simulations of hydrogen fluoride (HF) at pressures of 5-66 GPa along the 900 K isotherm. We predict a superionic phase at 33 GPa, where the fluorine atoms are fixed in a bcc lattice while the hydrogen atoms diffuse rapidly with a diffusion constant between 2 x 10(-5) and 5 x 10(-5)cm(2)s. We find that a transformation from asymmetric to symmetric hydrogen bonding occurs in HF at 66 GPa and 900 K. With superionic HF we have discovered a model system where symmetric hydrogen bonding occurs at experimentally achievable conditions. Given previous results on superionic H(2)O [Goldman et al., Phys. Rev. Lett. 94, 217801 (2005)] and NH(3) [Cavazzoni et al., Science 283, 44 (1999)], we conclude that high P, T superionic phases of electronegative element hydrides could be common.

Journal Article↗

PubMed2005

Atomistic simulations of spinodal phase separation preceding polymer crystallization.

Many polymeric materials crystallize when cooled below their melting temperature. Although progress has been made in our understanding of the crystallization process through both experimental and theoretical efforts, these studies have focused mainly on the crystal nucleation and growth mechanism, where critical nuclei are formed from a metastable state during the first stages of crystallization, leading ultimately to the growth of crystal domains. Attention has also been given to the structure during the precrystallization (induction period). A pretransition state occurring before crystallization has been characterized as an unstable phase separation initiated by density and orientational fluctuations. These fluctuations are caused by an increase in the average length of rigid trans segments along the polymer backbone during the induction period. These observations are consistent with the theory proposed in ref. 14 on the isotropic-to-nematic transition of polymer liquid crystals, that is, the parallel ordering of polymers is caused by an increase in chain rigidity. Here we use large-scale computer simulations to investigate melts of polymers in the early ordering stages (induction period) before crystallization. In the ordered domains we identify growing dense regions similar to smectic liquid crystals. Our simulations reveal a 'coexistence period' in the ordering before crystallization, where nucleation and growth mechanisms coexist with a phase-separation mechanism.

Crystallization↗

PubMed2005

New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid.

We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.

Journal Article↗

PubMed2005

Quantitative molecular thermochemistry based on path integrals.

The calculation of thermochemical data requires accurate molecular energies and heat capacities. Traditional methods rely upon the standard harmonic normal-mode analysis to calculate the vibrational and rotational contributions. We utilize path-integral Monte Carlo for going beyond the harmonic analysis and to calculate the vibrational and rotational contributions to ab initio energies. This is an application and an extension of a method previously developed in our group [J. Chem. Phys. 118, 1596 (2003)].

Journal Article↗

PubMed2005

Bonding in the superionic phase of water.

The predicted superionic phase of water is investigated via ab initio molecular dynamics at densities of 2.0--3.0 g/cc (34-115 GPa) along the 2000 K isotherm. We find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic O lattice with superionic proton conductivity is observed between 70 and 75 GPa, a much higher pressure than suggested in prior work. We find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, we find a solid superionic phase characterized by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-H hydrogen bonding with nearly 50% covalent character. In addition, we describe a metastable superionic phase with quenched O disorder.

Biophysics↗

PubMed2005

Dynamic ionization of water under extreme conditions.

Raman spectroscopy in a laser heated diamond anvil cell and first principles molecular dynamics simulations have been used to study water in the temperature range 300 to 1500 K and at pressures to 56 GPa. We find a substantial decrease in the intensity of the O-H stretch mode in the liquid phase with pressure, and a change in slope of the melting line at 47 GPa and 1000 K. Consistent with these observations, theoretical calculations show that water beyond 50 GPa is "dynamically ionized" in that it consists of very short-lived (<10 fs) H2O, H3O+, and OH- species, and also that the mobility of the oxygen ions decreases abruptly with pressure, while hydrogen ions remain very mobile. We suggest that this regime corresponds to a superionic state.

Journal Article↗

PubMed2005

Polymerization of formic acid under high pressure.

We report Raman, infrared, and x-ray diffraction (XRD) measurements, along with ab initio calculations on formic acid (FA) under pressure up to 50 GPa. We find an infinite chain Pna2(1) structure to be a high-pressure phase at room temperature. Our data indicate the symmetrization and a partially covalent character of the intrachain hydrogen bonds above approximately 20 GPa. Raman spectra and XRD patterns indicate a loss of long-range order at pressures above 40 GPa, with a large hysteresis upon decompression. We attribute this behavior to a three-dimensional polymerization of FA.

Journal Article↗

PubMed2004

Generation of methane in the Earth's mantle: in situ high pressure-temperature measurements of carbonate reduction.

We present in situ observations of hydrocarbon formation via carbonate reduction at upper mantle pressures and temperatures. Methane was formed from FeO, CaCO(3)-calcite, and water at pressures between 5 and 11 GPa and temperatures ranging from 500 degrees C to 1,500 degrees C. The results are shown to be consistent with multiphase thermodynamic calculations based on the statistical mechanics of soft particle mixtures. The study demonstrates the existence of abiogenic pathways for the formation of hydrocarbons in the Earth's interior and suggests that the hydrocarbon budget of the bulk Earth may be larger than conventionally assumed.

Journal Article↗

PubMed2004

Early chemistry in hot and dense nitromethane: molecular dynamics simulations.

We report density functional molecular dynamic simulations to determine the early chemical events of hot (T=3000 K) and dense (rho=1.97 g/cm(3), V/V(0)=0.68) nitromethane (CH(3)NO(2)). The first step in the decomposition process is an intermolecular proton abstraction mechanism that leads to the formation of CH(3)NO(2)H(+) and the aci ion H(2)CNO(2) (-). This event is also confirmed to occur in a fast annealing simulation to a final temperature of 4000 K at rho=2.20 g/cm(3). An intramolecular hydrogen transfer that transforms nitromethane into the aci acid form, CH(2)NO(2)H, accompanies this event. To our knowledge, this is the first confirmation of chemical reactivity with bond selectivity for an energetic material near the Chapman-Jouget state of the fully reacted material. We also report the decomposition mechanism followed up to the formation of H(2)O as the first stable product. We note that similarities in the global features of reactants, intermediates, and products of the reacting fluid seem to indicate a threshold for similar chemistry in the range of high densities and temperatures reported herein.

Journal Article↗

PubMed2004

Ab initio based force field and molecular dynamics simulations of crystalline TATB.

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.

Chemistry, Physical↗

PubMed2003

A method for tractable dynamical studies of single and double shock compression.

A new multiscale simulation method is formulated for the study of shocked materials. The method combines molecular dynamics and the Euler equations for compressible flow. Treatment of the difficult problem of the spontaneous formation of multiple shock waves due to material instabilities is enabled with this approach. The method allows the molecular dynamics simulation of the system under dynamical shock conditions for orders of magnitude longer time periods than is possible using the popular nonequilibrium molecular dynamics approach. An example calculation is given for a model potential for silicon in which a computational speedup of 10(5) is demonstrated. Results of these simulations are consistent with the recent experimental observation of an anomalously large elastic precursor on the nanosecond time scale.

Journal Article↗