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List of works by Karl Freed

A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations

scientific article published on 23 October 2018

A Probabilistic Graphical Model for Ab Initio Folding

scientific article (publication date: 2009)

A novel implicit solvent model for simulating the molecular dynamics of RNA

scientific article published on September 2013

A probabilistic and continuous model of protein conformational space for template-free modeling

scientific article (publication date: June 2010)

A simple method for faster nonbonded force evaluations

scientific article

A theory of interactions between polarizable dielectric spheres

scientific article published on 12 February 2016

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

Actin polymerization under pressure: a theoretical study

scientific article published on 01 January 2007

Advances in the generalized entropy theory of glass-formation in polymer melts

scientific article published on December 2014

All-atom fast protein folding simulations: the villin headpiece

scientific article published on 01 December 2002

An exactly solvable model of hierarchical self-assembly

scientific article published on 01 June 2009

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

scientific article published in April 2004

Analytical solution for steady-state populations in the self-assembly of microtubules from nucleating sites

scientific article published on 31 December 2002

Application of an efficient multireference approach to free-base porphin and metalloporphyrins: Ground, excited, and positive ion states ⬇️

scientific article published on August 28, 2011

Application of the entropy theory of glass formation to poly(alpha-olefins)

scientific article published on 01 September 2009

Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set ⬇️

scientific article published on August 17, 2011

Benchmarking all-atom simulations using hydrogen exchange

scientific article

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment

scientific article

Beyond Flory-Huggins Theory: New Classes of Blend Miscibility Associated with Monomer Structural Asymmetry

scientific article published in Physical Review Letters

Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

scientific article published in October 2015

Communication: The simplified generalized entropy theory of glass-formation in polymer melts

scientific article published in August 2015

Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion

scientific article published on 01 October 2014

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

scientific article published on 08 February 2017

Comparison of low-order multireference many-body perturbation theories

scientific article published in April 2005

Competition between self-assembly and surface adsorption

scientific article published in February 2009

Compressible models of equilibrium polymerization

scientific article published on 01 November 2005

Concentration fluctuations in miscible polymer blends: influence of temperature and chain rigidity

scientific article published on 01 May 2014

Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles ⬇️

scientific article published on September 14, 2012

Convergence behavior of multireference perturbation theory: Forced degeneracy and optimization partitioning applied to the beryllium atom

scientific article published on 01 July 1996

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

scientific article published on 13 April 2016

Cooperativity in self-limiting equilibrium self-associating systems

scientific article published on 01 November 2012

Crossover renormalization-group approach to semi-infinite inhomogeneous critical behavior

scientific article published on 01 September 1987

Crowding induced self-assembly and enthalpy-entropy compensation

scientific article published on 21 September 2009

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

scientific article (publication date: 23 October 2012)

Dense self-interacting lattice trees with specified topologies: From light to dense branching

scientific article published on 01 May 1992

Dielectric virial expansion of polarizable dipolar spheres

scientific article published on 01 October 2018

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

scientific article published in September 2005

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

scientific article published on 01 October 2006

Dynamics of electronic dephasing in the Fenna–Matthews–Olson complex

article published in 2010

Electronic structure of the calcium monohydroxide radical

scientific article published on 01 January 2005

Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins

scientific article

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

Entropy−Enthalpy Compensation in Chemical Reactions and Adsorption: An Exactly Solvable Model ⬇️

scientific article published on 02 February 2011

Equilibrium polymerization models of re-entrant self-assembly

scientific article published in April 2009

Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)].

scientific article published on August 2016

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar

scientific article published on 22 June 2015

Excluded volume effect on quasielastic neutron scattering from concentrated polymer solutions

Explanation for the Inversion of an UCST Phase Diagram to a LCST Diagram in Binary Polybutadiene Blends

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion

scientific article

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems

Flory-Huggins model of equilibrium polymerization and phase separation in the Stockmayer fluid

scientific article published on 28 January 2004

Folding and misfolding of the papillomavirus E6 interacting peptide E6ap

scholarly article

Fragility of glass-forming polymer liquids

scientific article published on 01 November 2005

General approach to polymer chains confined by interacting boundaries ⬇️

scientific article published on September 7, 2010

General approach to polymer chains confined by interacting boundaries. II. Flow through a cylindrical nano-tube ⬇️

scientific article published on October 14, 2011

General discussion

General discussion

General discussion

General discussion

Generalized Entropy Theory of Polymer Glass Formation

Generalized entropy theory of glass-formation in fully flexible polymer melts. ⬇️

scientific article published in December 2016

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

scientific article published on 01 April 2005

Geometry optimization of radicaloid systems using improved virtual orbital-complete active space configuration interaction (IVO-CASCI) analytical gradient method

scientific article published on 29 June 2010

Geometry optimization using improved virtual orbitals: a complete active space numerical gradient approach

scientific article published on 01 March 2007

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

scientific article published in July 2005

Image method for electrostatic energy of polarizable dipolar spheres.

scientific article

Image method for induced surface charge from many-body system of dielectric spheres.

scientific article published in September 2016

Improved virtual orbital multireference Møller-Plesset study of the ground and excited electronic states of protonated acetylene, C2H3+

scientific article published on 01 August 2008

Influence of Monomer Molecular Structure on the Miscibility of Polymer Blends

article

Influence of Stiffness, Monomer Structure, and Energetic Asymmetries on Polymer Blend Miscibilities: Applications to Polyolefins

Influence of monomer molecular structure on the glass transition in polymers I. Lattice cluster theory for the configurational entropy

Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model.

scholarly article

Influence of small rings on the thermodynamics of equilibrium self-assembly ⬇️

scientific article published on June 28, 2012

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

scientific article published in October 2017

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

scientific article

Ionic strength independence of charge distributions in solvation of biomolecules

scientific article published on December 2014

Langevin-Debye model for nonlinear electrostatic screening of solvated ions

scientific article published on 6 February 2009

Large-scale context in protein folding: villin headpiece

scientific article published on January 2003

Lattice Cluster Theory for Pedestrians: The Incompressible Limit and the Miscibility of Polyolefin Blends

article

Lattice cluster theory for dense, thin polymer films

scientific article published in April 2015

Lattice cluster theory for polymer melts with specific interactions ⬇️

scientific article published in July 2014

Lattice cluster theory of associating polymers. I. Solutions of linear telechelic polymer chains ⬇️

scientific article published on February 14, 2012

Lattice cluster theory of associating polymers. II. Enthalpy and entropy of self-assembly and Flory-Huggins interaction parameter χ for solutions of telechelic molecules ⬇️

scientific article published on February 14, 2012

Lattice cluster theory of associating polymers. IV. Phase behavior of telechelic polymer solutions

scientific article published on 01 May 2012

Lattice cluster theory of associating telechelic polymers. III. Order parameter and average degree of self-assembly, transition temperature, and specific heat ⬇️

scientific article published on May 21, 2012

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

scientific article published on 01 April 2006

Lattice model of equilibrium polymerization. VI. Measures of fluid "complexity" and search for generalized corresponding states

scientific article published on 01 December 2007

Lattice model of equilibrium polymerization. VII. Understanding the role of "cooperativity" in self-assembly

scientific article published on 01 June 2008

Lattice model of linear telechelic polymer melts. I. Inclusion of chain semiflexibility in the lattice cluster theory

scientific article published on 01 July 2015

Lattice model of linear telechelic polymer melts. II. Influence of chain stiffness on basic thermodynamic properties

scientific article published on 01 July 2015

Lattice theory for binding of linear polymers to a solid substrate from polymer melts. II. Influence of van der Waals interactions and chain semiflexibility on molecular binding and adsorption

scientific article published on 01 September 2019

Lattice theory for binding of linear polymers to a solid substrate from polymer melts: I. Influence of chain connectivity on molecular binding and adsorption

scientific article published on 01 September 2019

Lattice theory of competitive binding: Influence of van der Waals interactions on molecular binding and adsorption to a solid substrate from binary liquid mixtures

scientific article published on 01 July 2018

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

scientific article

Long-time dynamics of Met-enkephalin: comparison of theory with Brownian dynamics simulations

scientific article published on January 1999

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

scientific article

Mimicking the folding pathway to improve homology-free protein structure prediction.

scientific article

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

scientific article published on 01 November 2006

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

scientific article

Mixtures of lattice polymers with structured monomers

scientific article published on 01 April 2004

Mixtures of two self- and mutually-associating liquids: Phase behavior, second virial coefficients, and entropy-enthalpy compensation in the free energy of mixing

scientific article published in August 2017

Modeling large regions in proteins: Applications to loops, termini, and folding ⬇️

scientific article published on December 5, 2011

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering ⬇️

scientific article published on October 19, 2011

Modeling the hydration layer around proteins: HyPred

scientific article

Molecular Influences on Miscibility Patterns in Random Copolymer/Homopolymer Binary Blends ⬇️

scientific article published on July 28, 1998

Molecular applications of analytical gradient approach for the improved virtual orbital-complete active space configuration interaction method

scientific article published on January 2010

Molecular origins of cofilin-linked changes in actin filament mechanics

scientific article published on 24 January 2013

Multistep relaxation in equilibrium polymer solutions: a minimal model of relaxation in "complex" fluids

scientific article

New patterns of polymer blend miscibility associated with monomer shape and size asymmetry

On docking, scoring and assessing protein-DNA complexes in a rigid-body framework

scientific article

On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations

scientific article published on 17 September 2019

Perturbative many-body expansion for electrostatic energy and field for system of polarizable charged spherical ions in a dielectric medium

scientific article published in July 2014

Phase behavior and second osmotic virial coefficient for competitive polymer solvation in mixed solvent solutions

scientific article published on November 2015

Phase field method for nonequilibrium dynamics of reversible self-assembly systems

scientific article

Plasticization and antiplasticization of polymer melts diluted by low molar mass species

scientific article published in February 2010

Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors

scientific article published on 01 January 2007

Potential energy curve for isomerization of N2H2 and C2H4 using the improved virtual orbital multireference Møller-Plesset perturbation theory

scientific article published on 01 April 2008

Prediction of electronic structure of organic radicaloid anions using efficient, economical multireference gradient approach ⬇️

scientific article published on March 21, 2011

Protein structure prediction enhanced with evolutionary diversity: SPEED.

scientific article

Psi-constrained simulations of protein folding transition states: implications for calculating

scientific article published on March 2009

Quantifying the structural requirements of the folding transition state of protein A and other systems

scientific article published on July 2008

Quantum theory of the full pressure dependence of collision induced intersystem crossing

scientific article published on 15 December 1985

Reappraisal of cis effect in 1,2-dihaloethenes: an improved virtual orbital multireference approach.

scientific article

Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification

scientific article

Relation Between Solvent Quality and Phase Behavior of Ternary Mixtures of Polymers and Two Solvents that Exhibit Cononsolvency

scientific article published on 2 June 2016

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

scientific article published in May 2005

Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

scientific article published in Science

Role of monomer structure and compressibility on the properties of multicomponent polymer blends and solutions

article

Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds

scientific article published in June 2016

Self-assembly by mutual association: basic thermodynamic properties

scientific article published in December 2008

Self-assembly in a polymer matrix and its impact on phase separation

scientific article published on 01 March 2009

Simplified protein models: predicting folding pathways and structure using amino acid sequences

scientific article published on 11 July 2013

Small proteins fold through transition states with native-like topologies

scientific article published on 07 July 2006

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models

scientific article published on January 2008

Solvation of polymers as mutual association. I. General theory

scientific article published in April 2013

Solvation of polymers as mutual association. II. Basic thermodynamic properties

scientific article published on 01 April 2013

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

scientific article published on 30 August 2005

Surface-interaction exponents for surface susceptibility: Renormalization-group crossover for chi 1

scientific article published on 01 March 1985

The Descent into Glass Formation in Polymer Fluids ⬇️

scientific article published on January 5, 2011

The Folding Transition State of Protein L Is Extensive with Nonnative Interactions (and Not Small and Polarized) ⬇️

scientific article published on April 18, 2012

The glass transition temperature of polymer melts

scientific article published on 01 November 2005

The meaning of the "universal" WLF parameters of glass-forming polymer liquids

scientific article published in January 2015

Theoretical studies of the ground and excited state structures of stilbene

scientific article published on 12 April 2013

Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent

scientific article published on 01 June 2015

Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory

scientific article published on 01 June 2013

Toward a Molecular Basis for Understanding the Behavior of Isotopic Polymer Blends: Lattice Cluster Theory Computations for PSD/PSH Blends

article

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

scientific article published on 27 December 2018

Two coupled semi-infinite systems near criticality

scientific article published on 01 December 1986

Two glass transitions in miscible polymer blends?

scientific article published on 01 June 2014

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