Biomedical subjects

Karl F Freed

Publications and source records attributed to Karl F Freed.

At least 19 recordsLinked to original sources

PubMed2006

Minimal model of relaxation in an associating fluid: viscoelastic and dielectric relaxations in equilibrium polymer solutions.

Cluster formation and disintegration greatly complicate the description of relaxation processes in complex fluids. We systematically contrast the viscoelastic and dielectric properties for models of equilibrium polymers whose thermodynamic properties have previously been established. In particular, the monomer-mediated model allows chain growth to proceed only by monomer addition, while the scission-recombination model enables all particles to associate democratically, so that chain scission and fusion occur at the interior segments as well as at chain ends. The minimal models neglect hydrodynamic and entanglement interactions and are designed to explore systematically the competition between chemical reaction and internal chain relaxation and how this coupling modifies the dynamics from that of a polydisperse solution of Rouse chains with fixed lengths (i.e., "frozen" chains). As expected, the stress relaxation is nearly single exponential when the assembly-disassembly reaction is fast on the time scale of structural chain rearrangements, while multiexponential or nearly stretched exponential relaxation is obtained when this reaction rate is slow compared to the broad relaxation spectrum of almost unperturbed, nearly "dead" chains of intrinsically polydisperse equilibrium polymer solutions. More generally, a complicated intermediate behavior emerges from the interplay between the chemical kinetic events and internal chain motions.

Journal Article↗

PubMed2006

Does equilibrium polymerization describe the dynamic heterogeneity of glass-forming liquids?

A significant body of evidence indicates that particles with excessively high or low mobility relative to Brownian particles form in dynamic equilibrium in glass-forming liquids. We examine whether these "dynamic heterogeneities" can be identified with a kind of equilibrium polymerization. This correspondence is first checked by demonstrating the presence of a striking resemblance between the temperature dependences of the configurational entropy s(c) in both the theory of equilibrium polymerization and the generalized entropy theory of glass formation in polymer melts. Moreover, the multiple characteristic temperatures of glass formation are also shown to have analogs in the thermodynamics of equilibrium polymerization, supporting the contention that both processes are varieties of rounded thermodynamic transitions. We also find that the average cluster mass (or degree of polymerization) varies in nearly inverse proportionality to s(c). This inverse relation accords with the basic hypothesis of Adam-Gibbs that the number of particles in the cooperatively rearranging regions (CRR) of glass-forming liquids scales inversely to s(c) of the fluid. Our identification of the CRR with equilibrium polymers is further supported by simulations for a variety of glass-forming liquids that verify the existence of stringlike or polymeric clusters exhibiting collective particle motion. Moreover, these dynamical clusters have an exponential length distribution, and the average "string" length grows upon cooling according to the predictions of equilibrium polymerization theory. The observed scale of dynamic heterogeneity in glass-forming liquids is found to be consistent with this type of self-assembly process. Both experiments and simulations have revealed remarkable similarities between the dynamical properties of self-assembling and glass-forming liquids, suggesting that the development of a theory for the dynamics of self-assembling fluids will also enhance our understanding of relaxation in glass-forming liquids.

Journal Article↗

PubMed2006

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.

In order to investigate the level of representation required to simulate folding and predict structure, we test the ability of a variety of reduced representations to identify native states in decoy libraries and to recover the native structure given the advanced knowledge of the very broad native Ramachandran basin assignments. Simplifications include the removal of the entire side-chain or the retention of only the Cbeta atoms. Scoring functions are derived from an all-atom statistical potential that distinguishes between atoms and different residue types. Structures are obtained by minimizing the scoring function with a computationally rapid simulated annealing algorithm. Results are compared for simulations in which backbone conformations are sampled from a Protein Data Bank-based backbone rotamer library generated by either ignoring or including a dependence on the identity and conformation of the neighboring residues. Only when the Cbeta atoms and nearest neighbor effects are included do the lowest energy structures generally fall within 4 A of the native backbone root-mean square deviation (RMSD), despite the initial configuration being highly expanded with an average RMSD > or = 10 A. The side-chains are reinserted into the Cbeta models with minimal steric clash. Therefore, the detailed, all-atom information lost in descending to a Cbeta-level representation is recaptured to a large measure using backbone dihedral angle sampling that includes nearest neighbor effects and an appropriate scoring function.

Amino Acids↗

PubMed2006

Small proteins fold through transition states with native-like topologies.

The folding pathway of common-type acyl phosphatase (ctAcP) is characterized using psi-analysis, which identifies specific chain-chain contacts using bi-histidine (biHis) metal-ion binding sites. In the transition state ensemble (TSE), the majority of the protein is structured with a near-native topology, only lacking one beta-strand and an alpha-helix. psi-Values are zero or unity for all sites except one at the amino terminus of helix H2. This fractional psi-value remains unchanged when three metal ions of differing coordination geometries are used, indicating this end of the helix experiences microscopic heterogeneity through fraying in the TSE. Ubiquitin, the other globular protein characterized using psi-analysis, also exhibits a single consensus TSE structure. Hence, the TSE of both proteins have converged to a single configuration, albeit one that contains some fraying at the periphery. Models of the TSE of both proteins are created using all-atom Langevin dynamics simulations using distance constraints derived from the experimental psi-values. For both proteins, the relative contact order of the TS models is approximately 80% of the native value. This shared value viewed in the context of the known correlation between contact order and folding rates, suggests that other proteins will have a similarly high fraction of the native contact order. This constraint greatly limits the range of possible configurations at the rate-limiting step.

Computer Simulation↗

PubMed2006

Lattice model of equilibrium polymerization. V. Scattering properties and the width of the critical regime for phase separation.

Dynamic clustering associated with self-assembly in many complex fluids can qualitatively alter the shape of phase boundaries and produce large changes in the scale of critical fluctuations that are difficult to comprehend within the existing framework of theories of critical phenomena for nonassociating fluids. In order to elucidate the scattering and critical properties of associating fluids, we consider several models of equilibrium polymerization that describe widely occurring types of associating fluids at equilibrium and that exhibit the well defined cluster geometry of linear polymer chains. Specifically, a Flory-Huggins-type lattice theory is used, in conjunction with the random phase approximation, to compute the correlation length amplitude xi(o) and the Ginzburg number Gi corresponding, respectively, to the scale of composition fluctuations and to a parameter characterizing the temperature range over which Ising critical behavior is exhibited. Our calculations indicate that upon increasing the interparticle association energy, the polymer chains become increasingly long in the vicinity of the critical point, leading naturally to a more asymmetric phase boundary. This increase in the average degree of polymerization implies, in turn, a larger xi(o) and a drastically reduced width of the critical region (as measured by Gi). We thus obtain insight into the common appearance of asymmetric phase boundaries in a wide range of "complex" fluids and into the observation of apparent mean field critical behavior even rather close to the critical point.

Journal Article↗

PubMed2006

Entropy theory of polymer glass formation revisited. I. General formulation.

A generalized entropy theory of glass formation is developed by merging the lattice cluster theory for the thermodynamics of semiflexible polymer melts at constant pressure with the Adam-Gibbs relation between the structural relaxation time and the configurational entropy. Since experimental studies have suggested that the relative rigidity of the chain backbone and the side groups is an essential parameter governing the nature of glass formation in polymers, we incorporate this rigidity disparity parameter, along with monomer structure, into our new theoretical description of the polymer fluid thermodynamics. Our entropy theory is compared with alternative theories that describe the rate of structural relaxation in glass-forming liquids in terms of an activated rate process.

Journal Article↗

PubMed2005

The glass transition temperature of polymer melts.

We develop an analytic theory to estimate the glass transition temperature T(g) of polymer melts as a function of the relative rigidities of the chain backbone and side groups, the monomer structure, pressure, and polymer mass. Our computations are based on an extension of the semiempirical Lindemann criterion of melting to locate T(g) and on the use of the advanced mean field lattice cluster theory (LCT) for treating the thermodynamics of systems containing structured monomer, semiflexible polymer chains. The Lindemann criterion is translated into a condition for T(g) by expressing this relation in terms of the specific volume, and this free volume condition is used to calculate T(g) from our thermodynamic theory. The mass dependence of T(g) is compared to that of other characteristic temperatures of glass-formation. These additional characteristic temperatures are determined from the temperature variation of the LCT configurational entropy, in conjunction with the Adam-Gibbs model for long wavelength structural relaxation. Our theory explains generally observed trends in the variation of T(g) with polymer microstructure, and we find that T(g) can be tuned either upward or downward by increasing the length of the side chains, depending on the relative rigidities of the side groups and the chain backbone. The elucidation of the molecular origins of T(g) in polymer liquids should be useful in designing and processing new synthetic materials and for understanding the dynamics and controlling the preservation of biological substances.

Journal Article↗

PubMed2005

Fragility of glass-forming polymer liquids.

The fragility of polymeric glass-forming liquids is calculated as a function of molecular structural parameters from a generalized entropy theory of polymer glass-formation that combines the Adam-Gibbs (AG) model for the rate of structural relaxation with the lattice cluster theory (LCT) for polymer melt thermodynamics. Our generalized entropy theory predicts the existence of distinct high and low temperature regimes of glass-formation that are separated by a thermodynamically well-defined crossover temperature T(I) at which the product of the configurational entropy and the temperature has an inflection point. Since the predicted temperature dependence of the configurational entropy and structural relaxation time are quite different in these temperature regimes, we introduce separate definitions of fragility for each regime. Experimentally established trends in the fragility of polymer melts with respect to variations in polymer microstructure and pressure are interpreted within our theory in terms of the accompanying changes in the chain packing efficiency.

Journal Article↗

PubMed2005

Compressible models of equilibrium polymerization.

Flory-Huggins-type models of equilibrium polymerization are extended to describe compressible systems and, hence, the pressure dependence of thermodynamic properties. The theory is developed for three different mechanisms of equilibrium polymerization (the free association, monomer-activated polymerization, and chemically initiated polymerization models). In contrast to previous approaches for describing the pressure dependence, the theory delineates the thermodynamic consequences of the size disparities between solvent molecules, unpolymerized monomers, and the monomers within polymers. Basic thermodynamic properties (the extent of polymerization, density, heat capacities C(P) and C(V), etc.) are calculated analytically as functions of pressure, temperature, and composition of the associating species. Illustrative calculations refer to systems that polymerize upon cooling and demonstrate general agreement with numerous experimental trends. Comparisons with results from other theories are also discussed.

Journal Article↗

PubMed2005

Direct computation of characteristic temperatures and relaxation times for glass-forming polymer liquids.

Characteristic temperatures and structural relaxation times for different classes of glass-forming polymer liquids are computed using a revised entropy theory of glass formation that permits the chain backbone and the side groups to have different rigidities. The theory is applied to glass formation at constant pressure or constant temperature. Our calculations provide new insights into physical factors influencing the breadth of the glass transition and the associated growth of relaxation times.

Journal Article↗

PubMed2005

Statistical coil model of the unfolded state: resolving the reconciliation problem.

An unfolded state ensemble is generated by using a self-avoiding statistical coil model that is based on backbone conformational frequencies in a coil library, a subset of the Protein Data Bank. The model reproduces two apparently contradicting behaviors observed in the chemically denatured state for a variety of proteins, random coil scaling of the radius of gyration and the presence of significant amounts of local backbone structure (NMR residual dipolar couplings). The most stretched members of our unfolded ensemble dominate the residual dipolar coupling signal, whereas the uniformity of the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. Agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding.

Computational Biology↗

PubMed2005

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

A central issue in protein folding is the degree to which each residue's backbone conformational preferences stabilize the native state. We have studied the conformational preferences of each amino acid when the amino acid is not constrained to be in a regular secondary structure. In this large but highly restricted coil library, the backbone preferentially adopts dihedral angles consistent with the polyproline II conformation rather than alpha or beta conformations. The preference for the polyproline II conformation is independent of the degree of solvation. In conjunction with a new masking procedure, the frequencies in our coil library accurately recapitulate both helix and sheet frequencies for the amino acids in structured regions, as well as polyproline II propensities. Therefore, structural propensities for alpha-helices and beta-sheets and for polyproline II conformations in unfolded peptides can be rationalized solely by local effects. In addition, these propensities are often strongly affected by both the chemical nature and the conformation of neighboring residues, contrary to the Flory isolated residue hypothesis.

Computational Biology↗

PubMed2005

Relativistic effective valence shell Hamiltonian method: excitation and ionization energies of heavy metal atoms.

The relativistic effective valence shell Hamiltonian H(v) method (through second order) is applied to the computation of the low lying excited and ion states of closed shell heavy metal atoms/ions. The resulting excitation and ionization energies are in favorable agreement with experimental data and with other theoretical calculations. The nuclear magnetic hyperfine constants A and lifetimes tau of excited states are evaluated and they are also in accord with experiment. Some of the calculated quantities have not previously been computed.

Journal Article↗

PubMed2005

Generation of potential energy curves for the X1Sigma(+)g, B1Delta(+)g, and B'1Sigma(+)g states of C2 using the effective valence shell Hamiltonian method.

Calculations of the ground and excited state potential energy curves of C2 using the third-order effective valence Hamiltonian (Hv3rd) method are benchmarked against full configuration interaction and other correlated single-reference perturbative and nonperturbative theories. The large nonparallelity errors (NPEs) exhibited even by state-of-art coupled cluster calculations through perturbative triples indicate a serious deficiency of these single-reference theories. The Hv method, on the other hand, produces a much reduced NPE, rendering it a viable approximate many-body method for accurately determining global ground and excited state potential energy curvessurfaces.

Journal Article↗

PubMed2005

Comparison of low-order multireference many-body perturbation theories.

Tests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

Journal Article↗

PubMed2005

Electronic structure of the calcium monohydroxide radical.

Effective valence shell Hamiltonian H(v) calculations are used to map out three-dimensional potential energy surfaces for the 12 lowest electronic states of the CaOH radical. Excitation energies and spectroscopic constants are compared with experiment and prior computations where available, but many previously unavailable data are provided, including excited state dipole moments and oscillator strengths. Particular attention is paid to clarify the nature of nonlinear and quasilinear excited states, Renner-Teller couplings, and state mixings. The F (2)Pi and G (2)Pi (6 (2)A(') and 8 (2)A(')) states are both found to possess nonlinear local minima, due to an avoided crossing. Attention is also focused on the characteristics of basis sets necessary in high-accuracy calculations for the CaOH radical.

Journal Article↗

PubMed2005

A simple method for faster nonbonded force evaluations.

Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent "dielectric constant" in implicit solvent models. Benchmarks are provided for the all-atom, implicit solvent dynamics of Met-enkephalin, the villin headpiece, the B1 domain of protein-G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look-up tables for other implicit solvent models such as the generalized Born models.

Algorithms↗

PubMed2004

Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces.

Analytical solutions are derived for the density profiles and the free energies of compressible diblock copolymer melts (or incompressible copolymer solutions) near patterned surfaces. The density-functional self-consistent-field theory is employed along with a Gaussian chain model for bonding constraints and a random mixing approximation for nonbonded interactions. An analytical solution is rendered possible by expanding the chain distribution function around an inhomogeneous reference state with a nontrivial analytical solution, by retaining the linear terms, and by requiring consistency with the homopolymer limit. The density profiles are determined by both real and complex roots of a sixth-degree polynomial that may easily be obtained by solving a generalized eigenvalue problem. This analytical formulation enables one to efficiently explore the large nine-dimensional parameter space and can serve as a first approximation to computationally intensive studies with more detailed models. Illustrative computations are provided for uniform and patterned surfaces above the order-disorder transition. The results are consistent with the previous self-consistent-field calculations in that lamellar ordering appears near the surface above the order-disorder transition and the lamella order perpendicular or parallel to the surface depending on the commensurability between the periods of the surface pattern and the density oscillations.

Journal Article↗