Published in Science on June 07, 2002
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
Optical trapping. Rev Sci Instrum (2004) 7.15
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature (2005) 3.71
Direct observation of hierarchical folding in single riboswitch aptamers. Science (2008) 3.22
The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proc Natl Acad Sci U S A (2004) 3.18
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
High-resolution, single-molecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struct (2007) 2.58
Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc Natl Acad Sci U S A (2006) 2.48
Single-molecule biophysics: at the interface of biology, physics and chemistry. J R Soc Interface (2008) 2.06
Experimental free energy surface reconstruction from single-molecule force spectroscopy using Jarzynski's equality. Phys Rev Lett (2007) 1.95
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci U S A (2003) 1.76
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad Sci U S A (2003) 1.66
Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57
A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc Natl Acad Sci U S A (2002) 1.57
A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Nat Chem (2011) 1.43
Sub-angstrom conformational changes of a single molecule captured by AFM variance analysis. Biophys J (2006) 1.42
Force as a useful variable in reactions: unfolding RNA. Annu Rev Biophys Biomol Struct (2004) 1.39
Thermodynamic and kinetic aspects of RNA pulling experiments. Biophys J (2005) 1.38
Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys J (2004) 1.35
Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J Chem Phys (2009) 1.31
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
Folding and unfolding single RNA molecules under tension. Curr Opin Chem Biol (2008) 1.26
Mechanically probing the folding pathway of single RNA molecules. Biophys J (2003) 1.23
Biological mechanisms, one molecule at a time. Genes Dev (2011) 1.19
Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci U S A (2010) 1.19
Teaching the principles of statistical dynamics. Am J Phys (2006) 1.17
Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism. Nat Commun (2013) 1.15
Determination of thermodynamics and kinetics of RNA reactions by force. Q Rev Biophys (2006) 1.13
B-S transition in short oligonucleotides. Biophys J (2007) 1.11
Dissipative adaptation in driven self-assembly. Nat Nanotechnol (2015) 1.10
Optimized free energies from bidirectional single-molecule force spectroscopy. Phys Rev Lett (2008) 1.09
Determination of equilibrium free energy from nonequilibrium work measurements. Phys Chem Chem Phys (2010) 1.09
Forces guiding assembly of light-harvesting complex 2 in native membranes. Proc Natl Acad Sci U S A (2011) 1.07
Experimental test of Hatano and Sasa's nonequilibrium steady-state equality. Proc Natl Acad Sci U S A (2004) 1.06
Single Molecule Measurements of Interaction Free Energies Between the Proteins Within Binary and Ternary SNARE Complexes. J Nanoneurosci (2009) 1.06
Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation. Biophys J (2006) 1.00
Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex. Biophys J (2008) 1.00
Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at the single-molecule level. J Am Chem Soc (2010) 0.99
Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation. Proc Natl Acad Sci U S A (2007) 0.98
Exact low-force kinetics from high-force single-molecule unfolding events. Biophys J (2007) 0.97
Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods. Nucleic Acids Res (2012) 0.97
Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions. Nucleic Acids Res (2013) 0.96
Mechanism of titin unfolding by force: insight from quasi-equilibrium molecular dynamics calculations. Biophys J (2006) 0.96
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. J Chem Phys (2008) 0.96
Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF. Proc Natl Acad Sci U S A (2003) 0.95
Comparative energy measurements in single molecule interactions. Biophys J (2008) 0.94
Folding thermodynamics of pseudoknotted chain conformations. J Chem Phys (2006) 0.93
Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: theory and applications. Biophys J (2006) 0.93
Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing. Biopolymers (2011) 0.92
Free energy of membrane protein unfolding derived from single-molecule force measurements. Biophys J (2007) 0.92
G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA. Biophys J (2012) 0.91
Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl. PLoS One (2009) 0.90
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem (2013) 0.89
Density-dependent analysis of nonequilibrium paths improves free energy estimates. J Chem Phys (2009) 0.89
Using nonequilibrium measurements to determine macromolecule free-energy differences. Proc Natl Acad Sci U S A (2003) 0.87
Mechanical unfolding of two DIS RNA kissing complexes from HIV-1. J Mol Biol (2009) 0.86
Dynamic mechanisms for pre-miRNA binding and export by Exportin-5. RNA (2011) 0.84
Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. Elife (2015) 0.84
Mechano-transduction: from molecules to tissues. PLoS Biol (2014) 0.83
Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation. Nucleic Acids Res (2011) 0.83
Monte Carlo simulation for single RNA unfolding by force. Biophys J (2004) 0.83
RNA reactions one molecule at a time. Cold Spring Harb Perspect Biol (2010) 0.83
Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket. PLoS One (2011) 0.82
A stochastic, cantilever approach to the evaluation of solution phase thermodynamic quantities. Proc Natl Acad Sci U S A (2007) 0.81
A new computational approach for mechanical folding kinetics of RNA hairpins. Biophys J (2009) 0.81
Mechanisms of cellular proteostasis: insights from single-molecule approaches. Annu Rev Biophys (2014) 0.81
Single-molecule investigations of RNA dissociation. Biophys J (2004) 0.80
Statistical mechanics. Far from equilibrium. Science (2002) 0.80
Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins. Anal Chem (2013) 0.80
F-subunit reinforces torque generation in V-ATPase. Eur Biophys J (2014) 0.80
Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization. Eur Phys J E Soft Matter (2011) 0.79
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning. J Chem Phys (2015) 0.79
Coherence and measurement in quantum thermodynamics. Sci Rep (2016) 0.78
A single synthetic small molecule that generates force against a load. Nat Nanotechnol (2011) 0.78
ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Res (2015) 0.78
Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation. Pharmaceuticals (Basel) (2012) 0.77
Near-optimal protocols in complex nonequilibrium transformations. Proc Natl Acad Sci U S A (2016) 0.77
Temperature and chemical denaturant dependence of forced unfolding of titin I27. J Phys Chem B (2009) 0.77
Free-energy inference from partial work measurements in small systems. Proc Natl Acad Sci U S A (2014) 0.77
Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force. Nat Nanotechnol (2009) 0.77
Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules. Pharmaceuticals (Basel) (2013) 0.77
Force-induced lysozyme--HyHEL5 antibody dissociation and its analysis by means of a cooperative binding model. Biophys J (2010) 0.77
Stochastic thermodynamics of single enzymes and molecular motors. Eur Phys J E Soft Matter (2011) 0.76
Force unfolding single RNAs. Biophys J (2005) 0.76
Experimental and computational characterization of biological liquid crystals: a review of single-molecule bioassays. Int J Mol Sci (2009) 0.76
Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events. J Phys Chem B (2012) 0.75
Thermodynamic holography. Sci Rep (2015) 0.75
Direct evidence for three-dimensional off-axis trapping with single Laguerre-Gaussian beam. Sci Rep (2014) 0.75
Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics. Sci Rep (2016) 0.75
Multifractality of random eigenfunctions and generalization of Jarzynski equality. Nat Commun (2015) 0.75
Scaling Law for Irreversible Entropy Production in Critical Systems. Sci Rep (2016) 0.75
Probing the mechanisms of translation with force. Chem Rev (2014) 0.75
Optimal processes for probabilistic work extraction beyond the second law. Sci Rep (2016) 0.75
Local non-equilibrium thermodynamics. Sci Rep (2015) 0.75
On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols. PLoS One (2014) 0.75
Optimality and thermodynamics determine the evolution of transcriptional regulatory networks. Mol Biosyst (2011) 0.75
One-Particle Representation of Heat Conduction Described within the Scope of the Second Law. PLoS One (2016) 0.75
Passive water-lipid peptide translocators with conformational switches: from single-molecule probe to cellular assay. J Phys Chem B (2007) 0.75
Viscosity and drag force involved in organelle transport: investigation of the fluctuation dissipation theorem. Eur Phys J E Soft Matter (2013) 0.75
A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol (2005) 8.32
Ten years of tension: single-molecule DNA mechanics. Nature (2003) 7.20
Genomic scans for selective sweeps using SNP data. Genome Res (2005) 6.43
Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol (2004) 5.00
Recent and ongoing selection in the human genome. Nat Rev Genet (2007) 4.62
Direct observation of the three-state folding of a single protein molecule. Science (2005) 4.48
Following translation by single ribosomes one codon at a time. Nature (2008) 4.14
Structural transitions and elasticity from torque measurements on DNA. Nature (2003) 3.71
Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet (2010) 3.69
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature (2006) 3.67
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science (2009) 3.60
Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32
Recent advances in optical tweezers. Annu Rev Biochem (2008) 3.08
Intersubunit coordination in a homomeric ring ATPase. Nature (2009) 2.93
Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol (2003) 2.86
Mechanism of force generation of a viral DNA packaging motor. Cell (2005) 2.81
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature (2007) 2.64
Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc Natl Acad Sci U S A (2006) 2.48
Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol (2007) 2.39
Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet (2011) 2.34
Evolutionary history of GS3, a gene conferring grain length in rice. Genetics (2009) 2.33
ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell (2011) 2.31
DNA overwinds when stretched. Nature (2006) 2.27
DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell (2006) 2.25
Sequence-directed DNA translocation by purified FtsK. Science (2005) 2.22
Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A (2003) 2.15
Effect of force on mononucleosomal dynamics. Proc Natl Acad Sci U S A (2006) 2.03
Replication of mitochondrial DNA occurs by strand displacement with alternative light-strand origins, not via a strand-coupled mechanism. Genes Dev (2005) 1.94
Evidence for an upper limit to mitotic spindle length. Curr Biol (2008) 1.94
Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol (2007) 1.91
The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys Chem (2002) 1.90
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
Retracted The bacterial condensin MukBEF compacts DNA into a repetitive, stable structure. Science (2004) 1.83
Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A (2002) 1.77
The folding cooperativity of a protein is controlled by its chain topology. Nature (2010) 1.76
The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature (2011) 1.74
Laminin and biomimetic extracellular elasticity enhance functional differentiation in mammary epithelia. EMBO J (2008) 1.74
Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet (2012) 1.74
Temperature control methods in a laser tweezers system. Biophys J (2005) 1.70
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc Natl Acad Sci U S A (2003) 1.66
Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A (2005) 1.66
Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys J (2007) 1.61
Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A (2007) 1.59
Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis. Nat Struct Mol Biol (2008) 1.58
Proofreading dynamics of a processive DNA polymerase. EMBO J (2009) 1.58
Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM). Proc Natl Acad Sci U S A (2012) 1.56
Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci U S A (2010) 1.53
RNA folding and unfolding. Curr Opin Struct Biol (2004) 1.52
The ribosome modulates nascent protein folding. Science (2011) 1.51
NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork. Proc Natl Acad Sci U S A (2007) 1.50
Identification of the FtsK sequence-recognition domain. Nat Struct Mol Biol (2006) 1.49
Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A (2007) 1.49
Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology (2007) 1.48
How does a millimeter-sized cell find its center? Cell Cycle (2009) 1.48
Nucleosomal elements that control the topography of the barrier to transcription. Cell (2012) 1.46
Substrate interactions and promiscuity in a viral DNA packaging motor. Nature (2009) 1.41
How RNA unfolds and refolds. Annu Rev Biochem (2008) 1.37
High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell (2012) 1.35
SpoIIIE strips proteins off the DNA during chromosome translocation. Genes Dev (2008) 1.31
Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase. Science (2011) 1.31
Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J Mol Biol (2008) 1.29
Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. Eur Biophys J (2008) 1.29
Mechanochemistry of a viral DNA packaging motor. J Mol Biol (2010) 1.29
Unusual mechanical stability of a minimal RNA kissing complex. Proc Natl Acad Sci U S A (2006) 1.29
Relating single-molecule measurements to thermodynamics. Biophys J (2003) 1.26
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting. Proc Natl Acad Sci U S A (2009) 1.25
Characterization of the mechanical unfolding of RNA pseudoknots. J Mol Biol (2007) 1.20
Mechanics and structure of titin oligomers explored with atomic force microscopy. Biochim Biophys Acta (2003) 1.19
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol (2011) 1.19
Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA (2007) 1.17
Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc Natl Acad Sci U S A (2007) 1.15
Effect of protein structure on mitochondrial import. Proc Natl Acad Sci U S A (2005) 1.15
Determination of thermodynamics and kinetics of RNA reactions by force. Q Rev Biophys (2006) 1.13