quantitative & systems biology

bioinformatics & genomics

molecular biophysics

statistical physics

Quantitative & Systems Biology

G Guessous, V Patsalo, R Balakrishnan, T Çağlar, JR Williamson, T Hwa.
Inherited chitinases enable sustained growth and rapid dispersal of bacteria from chitin particles.
Nature Microbiol.  (2023).

M Mori, C Cheng, BR Taylor, H Okano, T Hwa.
Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions.
Nature Communication 14 : 4161 (2023).

BR Taylor, V Patsalo, H Okano, Y Shen, Z Zhang, JR Williamson, JD Rabinowitz, T Hwa.
A metabolic sum rule dictates bacterial response to short-chain fatty acid stress.
in submission (2022).

K Amarnath, AV Narla, S Pontrelli, J Dong, BR Taylor, T Caglar, J Schwartzman, U Sauer, OX Cordero, T Hwa.
Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance.
Nature Communication 14: 3165 (2023).

A Iffland-Stettner, H Okano, M Gralka, G Guessous, K Amarnath, OX Cordero, T Hwa, S Bonhoeffer.
A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01.
mSystems 8: e00377-22 (2023).

C Wu, M Mori, M Abele, A Banaei-Esfahani, Z Zhang, H Okano, R Aebersold, C Ludwig, T Hwa.
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves.
Nature Microbiol. 8: 347-359 (2023).

Matthew Scott and Terence Hwa.
Shaping bacterial gene expression by physiological and proteome allocation constraints.
Nature Reviews Microbiol. 21: 327-342 (2023).

R Balakrishnan, M Mori, I Segota, Z Zhang, R Aebersold, C Ludwig, T Hwa.
Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.
Science 378: 1066 (2022).  [news]

C Wu, R Balakrishnan, N Braniff, M Mori, G Manzanarez, Z Zhang, T Hwa.
Cellular perception of growth rate and the mechanistic origin of bacterial growth law
PNAS 119: e2201585119 (2022). [PNAS QnAs]

T Honda, J Cremer, L Mancini, Z Zhang, T Pilizota, T Hwa.
Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions
PNAS 119: e2110342119 (2022).

TTH Nguyen, EJ Zakem, A Ebrahimi, J Schwartzman, T Caglar, K Armanath, U Alcolombri, FJ Peaudecerf, T Hwa, R Stocker, OX Cordero, NM Levine.
Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates
Nature Communications 13: 1657 (2022).

Rohan Balakrishnan, Roshali T. de Silva, Terence Hwa, Jonas Cremer.
Suboptimal resource allocation in changing environments constrains response and growth in bacteria“.
Mol. Syst. Biol. 17: e10597 (2021).

Avaneesh V. Narla, Jonas Cremer, Terence Hwa.
A traveling wave solution for bacterial chemotaxis with growth.
PNAS 118: e2105138118 (2021).

Hugo Dourado, Matteo Mori, Terence Hwa, Martin J. Lercher.
On the optimality of the enzyme-substrate relationship in bacteria.
PLoS Biol. 19: e3001416 (2021).

Hiroyuki Okano, Rutger Hermsen, Terence Hwa.
Hierarchical and simultaneous utilization of carbon substrates: mechanistic insights, physiological roles, and ecological consequences.
Curr. Opin. Microb. 63: 172-178 (2021).

Mori M, Zhang Z, Banaei-Esfahani A, Lalanne JB, Okano H, Collins BC, Schmidt A, Schubert OT, Lee DS, Li GW, Aebersold R, Hwa T, Ludwig C.
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.
Mol Syst Biol. 17: e9536 (2021).

Karl Kochanowski, Hiroyuki Okano, Vadim Patsalo, James R. Williamson, Uwe Sauer, Terence Hwa.
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation.
Mol. Syst. Biol. 17: e10064 (2021).

Markus Basan, Tomoya Honda, Dimitris Christodoulou, Manuel Hoerl, Yu-Fang Chang, Emanuele Leoncini, Avis Mukherjhee, Hiroyuki Okano, Brian R. Taylor, Josh M. Silverman, Carlos Sanchez, James R. Williamson, Johan Paulsson, Terence Hwa, Uwe Sauer.
A universal tradeoff between growth and lag in fluctuating environment.
Nature 584: 470-474 (2020).

Terence Hwa. “Cell behavior and control”,
in The Physics of Living Matter: Space, Time, and Information in Biology, Proceeding of the 27th Solvay Conference on Physics. D.J. Gross, A. Sevrin, B. Shraiman, Eds. (World Scientific, 2020);

Hai Zheng, Yang Bai, Meiling Jiang, Taku Tokuyasu, Xiongliang Huang, Falun Zhong, Xiongfei Fu, Nancy Kleckner, Terence Hwa, Chenli Liu.
General quantitative relations linking cell growth and the cell cycle in E. coli.
Nature Microbiol. 5:995-1001 (2020).

Hiroyuki Okano, Rutger Hermsen, Karl Kowchanowski, Terence Hwa.
Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Eschericihia coli.
Nature Microbiology 5:206-215 (2020).

Jonas Cremer, Tomoya Honda, Ying Tang, Jerome Wong-Ng, Massimo Vergassola, Terence Hwa.
Chemotaxis as a navigation strategy to thrive in nutrient-replete environments.
Nature  575: 658-663 (2019). [News & Views, Nature] [ScienceDaily] [Research highlight, Nature Reviews Microbiology]

Weirong Liu, Jonas Cremer, Dengjin Li, Terence Hwa, Chenli Liu.
An evolutionary stable strategy to colonize spatially extended habitats,
Nature 575: 664-668 (2019). [News & Views, Nature] [ScienceDaily] [Research highlight, Nature Reviews Microbiology]

Manlu Zhu, Matteo Mori, Terence Hwa, Xiongfeng Dai.
Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination,
Nature Microbiology 4: 2347-2356 (2019).

Mya R. Warren, Hui Sun, Yue Yan, Jonas Cremer, Bo Li, and Terence Hwa.
Spatiotemporal establishment of dense bacterial colonies growing on hard agar,
eLife 8: e41093 (2019).

Xiongfeng Dai, Manlu Zhu, Mya Warren, Rohan Balakrishnan, Hiroyuki Okano, James R. Williamson, Kurt Fredrick, Terence Hwa.
Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress,
mBio 9: e02375-17 (2018).

Markus Arnoldini, Jonas Cremer, Terence Hwa.
Bacterial growth, flow, and mixing shape human gut microbiota density and composition,
Gut Microbes: 1-17 (2018).

David Erickson, Severin Schink, Vadim Patsalo, James R. Williamson, Ulrich Gerland, Terence Hwa.
A global resource allocation strategy governs growth transition kinetics of E. coli”,
Nature 551: 119–123 (2017). [Press release] [News]

Matteo Mori, Severin Schink, David Erickson, Ulrich Gerland, Terence Hwa.
Quantifying the benefit of a proteome reserve in fluctuating environments”,
Nature Communications 8: 1225 (2017).

Jonas Cremer, Markus Arnoldini, Terence Hwa.
Effect of water flow and chemical environment on microbiota growth and composition in the human colon”,
PNAS 114: 64538-43 (2017).

Xiongfeng Dai, Manlu Zhu, Mya Warren, Rohan Balakrishnan, Vadim Patsalo, Hiroyuki Okano, James R. Williamson, Kurt Fredrick, Yi-ping Wang, Terence Hwa.
Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth“,
Nature Microbiology 2: 16231 (2017).

Jonas Cremer, Igor Segota, Chih-yu Yang, Markus Arnoldini, John T. Sauls, Zhongge Zhang, Edgar Gutierrez, Alex Groisman, Terence Hwa.
The effect of flow and peristaltic mixing on bacterial growth in a gut-like channel“,
PNAS 113: 11414-9 (2016).

Matteo Mori, Terence Hwa, Olivier C. Martin, Andreas de Martino, Enzo Marinari.
Constrained Allocation Flux Balance Analysis“,
PLoS Comp. Biol. 12: e1004913 (2016).

Markus Basan,  Sheng Hui, Hiroyuki Okano, Zhongge Zhang, Yang Shen, James R. Williamson, Terence Hwa.
Overflow metabolism in E. coli results from efficient proteome allocation“,
Nature 528: 99-104 (2015). [BBC News] [Science Daily] [Scientific American]

Markus Basan, Manlu Zhu, Xiongfeng Dai, Mya Warren, Daniel Sévin, Yi-Ping Wang, Terence Hwa.
Inflating bacterial cells by increased protein expression“,
Mol. Syst. Biol. 11: 836 (2015).

Rutger Hermsen, Hiroyuki Okano, Conghui You, Nicole Werner, Terrence Hwa.
“A growth-rate composition formula for the growth of E. coli on co-utilized carbon substrates”,
Mol Syst Biol. 11: 801-806 (2015).

Sheng Hui, Josh Silverman, Stephen Chen, David Erickson, Markus Basan, Jilong Wang, Terence Hwa, James R. Williamson.
“Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria”,
Mol Syst Biol. 11: 786-799 (2015).

Stefan Klumpp, Terence Hwa.
“Bacterial growth: global effects on gene expression, growth feedback and proteome partition.” 
Curr. Op. Biotech 28: 96-102 (2014).

Chi Wa Cheng, Ben Niu, Mya Warren, Larysa H. Pevny, Robin Lovell-Badge, Terence Hwa, Kathryn Cheah.
“Predicting the spatiotemporal dynamics of hair follicle patterns in the developing mouse.”
PNAS 111: 2596-2601 (2014).

Matthew Scott, Stefan Klumpp, Eduard Mateescu, Terence Hwa.
“Emergence of robust growth laws from optimal regulation of ribosome synthesis”.
Mol Syst Biol 10: 747-760 (2014),

Faruck Morcos, Terence Hwa, José Onuchic, Martin Weigt.
“Direct coupling analysis for protein contact prediction”,
Methods Mol Biol 1137: 55-70 (2014).

J. Barrett Deris, Minsu Kim, Zhongge Zhang, Hiroyuki Okano, Rutger Hermsen, Alexander Groisman, Terence Hwa
“The innate growth bistability of antibiotic resistant bacteria.”
Science 342: 1237435 (2013). [Supplementary Materials] 
[ScienceDaily News] [Inside Science]

Faruck Morocs, Biman Jana, Terence Hwa, Jose Onuchic.
“Co-evolutionary signals across protein lineages help capture multiple protein conformations.”
PNAS 110: 20533-20538 (2013).

Stefan Klumpp, Matthew Scott, Steen Pedersen, Terence Hwa.
“Molecular crowding limits translation and cell growth”,
PNAS 110: 16754-16759 (2013).
[ScienceDaily News]

C. You, H. Okano, S. Hui, Z. Zhang, M. Kim, C. W. Gunderson, Y.-P. Wang, P. Lenz, D. Yan & T. Hwa
“Coordination of bacterial proteome with metabolism by cyclic AMP signalling”
Nature 500: 301-306 (2013). [Supplementary Information]
[Nature News & Views][Physics Today Search & Discovery][ScienceDaily News]

S. Klumpp, J. Dong, T. Hwa
“On ribosome load, codon bias and protein abundance”
PLoS One 7: e48542 (2012).

M. Kim, Z. Zhang, H. Okano, D. Yan, A. Groisman, and T. Hwa.
“Need-based activation of ammonium uptake in Escherichia coli
Mol. Syst. Biol. 8: 616 (2012). .

R. Hermsen, J. B. Deris, and T. Hwa.
“On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient”
PNAS 109: 10775-10780 (2012). [Highlight from PNAS] [UC Health] [Physics Today Update]

J.I. Sulkowska, F. Morcos, M. Weigt, T. Hwa, and J.N. Onuchic.
Genomics-aided structure prediction“,
PNAS 109: 10340-10345 (2012).

X. Fu, L.H. Tang, C. Liu, J.D. Huang, T. Hwa, and P. Lenz.
Stripe formation in bacterial systems with density-suppresed motility“,
Phys. Rev. Lett. 108 198102 (2012).

F. Morcos, A. Pagnini, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, and M. Weigt.
Direct-coupling analysis of residue co-evolution captures native contacts across many protein families“,
PNAS 108: E1293-1301 (2011).

C. Liu, X. Fu, L. Liu, X. Ren, C.K.L. Chau, S. Li, L. Xiang, H. Zeng, G. Chen, L.H. Tang, P. Lenz, X. Cui, W. Huang, T. Hwa, and J.D. Huang
Sequential establishment of stripe patterns in an expanding cell population
Science 334: 238-241 (2011).  [Science Daily][Physics Today]

P. McHale, C. M. Mizutani, D. Kosman, D. L. MacKay, M. Belu, W. McGinnis, E. Bier, and T. Hwa.
“Differential response to a morphogen gradient mediated by gene-length associated transcriptional delay”, [cover page]
Develop. Biol. 360: 230-40 (2011).

R. Hermsen, D.W. Erickson, and T. Hwa.
Speed, sensitivity, and bistability in auto-activating signaling circuits
PLoS Comp. Biol. 7: e1002265 (2011).

D. Yan, P. Lenz, and T. Hwa.
Quantification of intracellular 2-oxoglutarate levels in E. coli: Overcoming fluctuation and leakage problems
Appl. Environ. Microbiol. 77: 6763-6771 (2011).

Y. Hao, Z.J. Zhang, D.W. Erickson, M. Huang, Y. Huang, J. Li, T. Hwa, and H. Shi.
Quantifying the sequence-function relation in gene silencing by bacterial small RNAs“,
PNAS 108: 12473-12478 (2011).

M. Scott and T. Hwa
Bacterial growth laws and their applications“,
Curr Op Biotech. 22: 559-565 (2011).

A. Procaccini, B. Lunt, H. Szurmant, T. Hwa, and M. Weigt.
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and Crosstalks”,
PLoS One: e19729 (2011).

M. Scott, C. W. Gunderson, E. Mateescu, Z. Zhang and T. Hwa
“Interdependence of cell growth and gene expression: origins and consequences”,
Science 330: 1099-1102 (2010). [Supporting Onilne Material]
[Perspective in Science][Physics Today][Chem & Engr News]

R. Hermsen and T. Hwa
“Sources and sinks: a stochastic model of evolution in heterogeneous environments”,
Phys. Rev. Lett. 105: 248104 (2010). [highlight in Physics]

H. Okano, T. Hwa, P. Lenz, D. Yan
“Reversible Adenylylation of Glutamine Synthetase is Dynamically Counterbalanced during Steady-State Growth of Escherichia coli”,
J. Mol. Biol. 404: 522-536 (2010).

A. Schug, M. Weigt, J.N. Onuchic, T. Hwa, and H. Szurmant
“High resolution protein complexes from integrating genomic information with molecular simulation”,
PNAS 106: 22124-22129 (2009).

S. Klumpp, Z. Zhang and T. Hwa
“Growth-rate dependent global effects on gene expression in bacteria” ,
Cell 139: 1366-1375 (2009).

E. Levine, M. Huang, Y.W. Huang, T. Kuhlman, H. Shi, Z. Zhang, and T. Hwa
On Noise and Silence in small RNA regulation”,

S. Klumpp and T. Hwa
“Traffic patrol in the transcription of ribosomal RNA”,
RNA Biology 6: 392-394 (2009).

U. Gerland and T. Hwa
“Evolutionary Selection Between Deifferent Modes of Gene Regulation”,
PNAS 106 : 8841-846 (2009). [PNAS highlight]

M. Weigt, R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
“Identification of direct residue contacts in protein-protein interaction by message passing”
PNAS 106 : 67-72 (2009).

S. Klumpp and T. Hwa
“Growth-rate dependent partitioning of RNA polymerases in bacteria”,
PNAS 105: 20245-20250 (2008).

E. Levine and T. Hwa
Small RNAs establish gene expression thresholds
Curr. Op. Microbial. 11: 574-579 (2008).

S. Klumpp and T. Hwa
“Stochasticity and traffic jams in the transcription of ribosomal RNA: Novel role of termination and antitermination”,
PNAS 105: 18159-18164 (2008).

J. Liu, A. Desai, J. N. Onuchic, T. Hwa
“An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis”,
PNAS 105: 13752-7 (2008).

J. Liu, A. Desai, J. N. Onuchic, T. Hwa
“A Mechano-biochemical mechanism for Mono-oriented Chromosome Oscillation in Mitosis”,
PNAS 104: 16104-9 (2007).

G. Fritz, N.E. Buchler, T. Hwa, and U. Gerland
“A Genetic Circuit for Epigenetic Memory”
Syst Synth Biol 1: 89-98 (2007).

E. Levine, Z. Zhang, T. Kuhlman, and T. Hwa
“Quantitative Characteristics of Gene Regulation Mediated by small RNA” ,
PLoS Biol 5: e229 (2007).

E. Levine and T. Hwa
“Stochastic Fluctuations in Metabolic Pathways”
PNAS 104: 9244-9249 (2007).

M. Scott, T. Hwa, B. Ingalls
“Deterministic Characterization of Stochastic Genetic Circuits”
PNAS 104: 7402-7407 (2007).

T. Kuhlman, Z. Zhang, M. Saier, Jr, and T. Hwa
“Quantitative Characterization of Combinatorial Transcriptional Control of the lactose operon of E. coli” 
PNAS 104: 6043-6048 (2007).

N.E. Buchler, U. Gerland, and T. Hwa
“Nonlinear protein degradation on the funtions of genetic circuits”
PNAS 102 : 9559-9564 (2005).

L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, R. Philips
“Transcriptional Regulation by the Numbers: Applications”
Curr. Op. Genet. Dev. 15 : 125-135 (2005).

L. Bintu, N.E. Buchler, H. Garcia, U. Gerland, T. Hwa, J. Kondev, R. Philips
“Transcriptional Regulation by the Numbers: Models”
Curr. Op. Genet. Dev. 15 : 116-124 (2005).

T. Hwa
“A genetic switch: New lessons from a classic system”
Science 305: 345 (2004).

W. Peng, H. Levine, T. Hwa, and David A. Kessler
“Analytical study of the effect of recombination on evolution via DNA shuffling”
Phys. Rev. E 69: 051911 (2004).

N. Buchler, U. Gerland and T. Hwa
“On Schemes of Combinatorial Transcription Control”
PNAS 100: 5136-5141 (2003).

W. Peng, U. Gerland, T. Hwa and H. Levine,
“Dynamics of Competitive Evolution on a Smooth Landscape”
Phys. Rev. Lett. 90: 088103 (2003).

U. Gerland and T. Hwa
“On the Selection and Evolution of Regulatory DNA Motifs”
J. Mol. Evol 55: 386-400 (2002).

U. Gerland, J.D. Moroz and T. Hwa,
“Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction”
PNAS 99: 12015-12020 (2002).

Bioinformatics & Genomics

A. Schug, M. Weigt, J. Hoch, J. Onuchic, T. Hwa and H. Szurmant
“Computational Modeling of Phosphotransfer Complexes in Two-Component Signaling”
Methods in Enzymology, 471: 43-58 (2010).

B. Lunt, H. Szurmant, A. Procaccini, J. Hoch, T. Hwa, and M. Weigt,
“Inference of Direct Residue Contacts in Two-Component Signaling”
Methods in Enzymology, 471: 17-41 (2010).

M. Weigt, R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
“Identification of direct residue contacts in protein-protein interaction by message passing”
PNAS 106 : 67-72 (2009).

R.A. White, H. Szurmant, J.A. Hoch, and T. Hwa
“Features of Protein-protein Interactions in Two-component Signaling deduced from Genomic Libraraies “
Methods in Enzymology 422: 75-101 (2007).

M. Lipatov, P.F. Arndt, T. Hwa, and D.A. Petrov
“A Novel  Method Distinguishes Between Mutation Rates and Fixation Biases in Patterns of Single-Nucleotide Substitution”
J. Mol. Evol. 62: 168-175 (2006).
P.F. Arndt, T. Hwa, and D.A. Petrov
“Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specfic effects”
J. Mol. Evol. 60: 748-763 (2005).

P.F. Arndt and T. Hwa
“Identification and Measurement of Neighbor Dependent Nucleotide Substitution Processes”
Bioinformatics 21: 2322-2328 (2005).

P.F. Arndt and T. Hwa
“Regional and time-resolved mutation patterns of the human genome” 
Bioinformatics 20: 1482-1485 (2004).

P.F. Arndt, D.A. Petrov and T. Hwa
“Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation”
Mol. Biol. Evol. 20: 1887-1896 (2003).

P.F. Arndt, C.B. Burge and T. Hwa,
“DNA Sequence Evolution with Neighbor-Dependent Mutation”
J Comput Biol. 10: 313-22 (2003).

Y.-k. Yu, R. Bundschuh, and T. Hwa,
“Hybrid Alignment: High Performance with Universal Statistics”
Bioinformatics 18: 865-872 (2002).

R. Sasik, N. Iranfar, T. Hwa, W.F. Loomis,
“Extracting Transcriptional Events from the Temporal Gene Expression Patterns during Dictyostelium Development”
Bioinformatics 18: 61-66 (2002).

Y.-k. Yu, R. Bundschuh, and T. Hwa,
“Statistical Significance and Extreme Ensemble of Gapped Local Hybrid Alignment”
in Biological Evolution and Statistical Physics (Lecture Notes in Physics, vol 585)
M. Lassig and A. Valleriani eds.,  3-21 (Springer-Verlag, Berlin, 2002).

N. Iranfar, D. Fuller, R. Sasik, T. Hwa, M. Laub, W.F. Loomis,
“Expression Patterns of Cell-type Specific Genes in Dictyostelium”
Mol. Biol. Cell 12: 2590-2600 (2001).

R. Sasik, T. Hwa, N. Iranfar, and W. F. Loomis,
“Percolation Clustering: A Novel Approach Applied to the Clustering
of Gene Expression Patterns in Dictyostelium Development”

Proceedings of the Pacific Symposium on Biocomputing,
R. B. Altman et al. eds, 335-347 (World Scientific, Singapore, 2001).

Y.-k. Yu and T. Hwa,
“Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models”
J. Comp. Biol. 8, 249-282 (2001).

S. Altschul, R. Bundschuh, R. Olsen and T. Hwa,
“The Estimation of Statistical Parameters for Local Alignment Score Distributions”
Nucleic Acids Research 29,  351–361 (2001).

D. Drasdo, T. Hwa and M. Lassig,
“Scaling Laws and Similarity Detection in Sequence Alignment with Gaps”
J. Comp. Biol. , 115-141 (2001).

R. Bundschuh and T. Hwa,
“An Analytical Study of the Phase Transition Line in Local Sequence Alignment with Gaps”
Discrete Applied Math. 104, 113-142, (2000).

T. Hwa,
“From Mesoscopic Vortex Physics to Genomics”
Nature 399, 17-19 (1999).

R. Olsen, R. Bundschuh and T. Hwa,
“Rapid Assessment of Extremal Statistics for Gapped Local Alignment”
in Proceedings of The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB99),
T. Lengauer et al. eds., 211–222 (AAAI Press, Menlo Park, 1999).

R. Olsen, T. Hwa and M. Lassig,
“Optimizing Smith-Waterman Alignments”
in Pacific Symposium on Biocomputing 4, 302-313 (1999).

D. Drasdo, T. Hwa and M. Lassig,
“A Statistical Theory of Sequence Alignment with Gaps”
in Proceedings of The Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98),
J. Glasnow et al. eds, 52-58 (AAAI Press, Menlo Park, 1998).

T. Hwa and M. Lassig,
“Optimal Detection of Sequence Similarity by Local Alignment”
in Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB98),
S. Istrail, P. Pevzner, and M.S. Waterman eds, 109-116 (ACM Press, 1998).

T. Hwa,
“From Flux Pinning to DNA Sequence Alignment”,
Quantum Coherence and Decoherence, K. Fujikawa and Y. A. Ono eds,
109-114 (Elsevier, Amsterdam, 1996).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa and M. Lassig,
“Similarity-Detection and Localization,”
Phys. Rev. Lett. 76, 2591-2594 (1996). 
[Abstract in HTML format]
 [Document in Postscript format]

Molecular Biophysics

U. Gerland, R. Bundschuh, T. Hwa
“Using nanopores to learn RNA structures”
Phys. Biol. 1: 19-27, (2004).

U. Gerland, R. Bundschuh and T. Hwa,
“Mechanically probing the folding pathway of single RNA molecules”
Biophys. J. 84: 2831-2840 (2003).

T. Hwa, E. Marinari, K. Sneppen and L.-H. Tang,
“Localization of denaturation bubbles in heterogeneous DNA sequences”
PNAS 100: 4411-4416 (2003).

R. Bundschuh and T. Hwa,
“Statistical Mechanics of secondary structures formed by random RNA sequences”
Phys. Rev. E 65: 031903 (2002).

R. Bundschuh and T. Hwa,
“Phases of the Secondary Structures of RNA Sequences”
Europhys. Lett.
 59: 903-909 (2002).

U. Gerland, R. Bundschuh, and T. Hwa,
“Force-induced Denaturation of RNA”
Biophys. J. 81, 1324-1332 (2001).

R. Bundschuh and T. Hwa,
“RNA Structure Formation: A Solvable Model of Heteropolymer Folding”
Phys. Rev. Lett. 83, 1479-1482 (1999).

D. Cule and T. Hwa,
“Polymer Reptation in Disordered Media”,
Phys. Rev. Lett. 80, 3145-3148 (1998).

D. Cule and T. Hwa,
“Denaturation of Heterogeneous DNA”,
Phys. Rev. Lett. 79, 2375-2378 (1997).

Statistical Physics

C. Zeng, P. Leath and T. Hwa,
“Universal Susceptibility Variations in 1+1 Dimensional Vortex Glass”
Physica C 332, 232-236 (2000).

B. Boghosian, C.C. Chow and T. Hwa,
“Hydrodynamics of the Kuramoto-Sivashinsky Equation in Two Dimensions”
Phys. Rev. Lett. 83, 5262-5265 (1999).

C. Zeng, P. Leath and T. Hwa,
“Thermodynamics of Mesoscopic Vortex Systems in 1+1 Dimensions”
Phys. Rev. Lett. 83, 4860-4863 (1999).

D. Cule and T. Hwa,
“Static and Dynamic Properties of Inhomogeneous Elastic Media on Disordered Substrate”,
Phys. Rev. B 57, 8235-8253 (1998).

M.A. Munoz and T. Hwa,
“On Nonlinear Diffusion with Multiplicative Noise”,
Europhys. Lett. 41, 147-152 (1998).

T. Hwa and D. Cule,
“Polymer Adsorption on Disordered Substrates”
Phys. Rev. Lett. 79, 4930 (1997).

J. Kierfeld, T. Natterman and T. Hwa,
“Topological Order in Vortex Glass Phases of Type-II Superconductors,”
Phys. Rev. B 55, 626-629 (1997).
[Abstract in HTML format] [Document in Postscript format]

J. Kierfeld and T. Hwa,
“Interacting Arrays of Steps and Lines in Random Media,”
Phys. Rev. Lett. 77, 4233-4236 (1996).
[Abstract in HTML format] [Document in Postscript format]

D. Cule and T. Hwa,
“Tribology of Sliding Elastic Media,”
Phys. Rev. Lett. 77, 278-281 (1996).
[Abstract in HTML format] [Document in Postscript format]

E. Frey, U. C. Tauber and T. Hwa,
“Mode-Coupling and Renormalization Group Results for the noisy-Burgers’ Equations,”
Phys. Rev. E 53, 4424-4438 (1996).
[Abstract in HTML format] [Document in Postscript format]

C. C. Chow and T. Hwa,
“Defect-Mediated Stability: An Effective Hydrodynamic Theory of Spatio-Temporal Chaos,”
Physica D 84, 494-512 (1995).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa,
“Flux Pinning in High-Temperature Superconductors,”
McGraw-Hill 1995 Yearbook on Science & Technology .
[Abstract in HTML format] [Document in Postscript format]

T. Hwa and T. Nattermann,
“Disorder-Induced Depinning Transition,”
Phys. Rev. B 51, 455-469 (1995).
[Abstract in HTML format] [Document in Postscript format]

G. G. Batrouni and T. Hwa,
“Dynamic and Static Properties of Randomly Pinned Planar Flux Array,”
Phys. Rev. Lett. 72, 4133-4136 (1994).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa and D. S. Fisher,
“Vortex Glass Phase and Universal Susceptibility Variations in Planar Arrays of Flux Lines,”
Phys. Rev. Lett. 72, 2466-2469 (1994).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa and D. S. Fisher,
“Anomalous Fluctuations of Directed Polymers in Random Media,”
Phys. Rev. B 49, 3136-3154 (1994).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa, P. le Doussal, D. R. Nelson and V. M. Vinokur,
“Enhanced Flux Pinning and Forced Entanglement in High Temperature Superconductors with Randomly Splayed Columnar Defects,”
Phys. Rev. Lett. 71, 3545-3548 (1993).
[Abstract in HTML format] [Document in Postscript format]

T. Hwa, D. R. Nelson and V. M. Vinokur,
“Flux Line Pinning by Competing Disorders,”
Phys. Rev. B 67, 1167-1174 (1993).

M. Paczuski, M. Barma, S. N. Majumdar and T. Hwa,
“Fluctuations of a Stationary Nonequilibrium Interface,”
Phys. Rev. Lett. 69, 2735 (1992).

T. Hwa,
“Nonequilibrium Dynamics of Driven Line Liquids,”
Phys. Rev. Lett. 69, 1552-1555 (1992).

G. Grinstein, T.Hwa and H.J. Jensen,
“1/f-Noise in Dissipative Transport,”
Phys. Rev. A 45, R559-562 (1992).

X. Wen, C. W. Garland, T. Hwa, M. Kardar, E. Kokufuta, Y. Li, M. Orkisz and T. Tanaka,
“Crumpled and Collapsed Conformations in Solid Membranes,”
Nature 355, 426 (1992).

T. Hwa and M. Kardar,
“Avalanches, Hydrodynamics, and Great Events in Models of Sandpiles,”
Phys. Rev. A 45, 7002 (1992).

T. Hwa, M. Kardar and M. Paczuski,
“Growth-Induced Roughening of Crystalline Facets,”
Phys. Rev. Lett. 66, 441-444 (1991).

T. Hwa, E. Kokufuta and T. Tanaka,
“Conformation of Graphite-Oxide Membranes in Solution,”
Phys. Rev. A 44, R2235-2238 (1991).

B. Duplantier, T. Hwa and M. Kardar,
“Renormalizability of the Self-Avoiding Tethered Manifolds,”
Phys. Rev. Lett. 64, 2022-2025 (1990).

T. Hwa,
“Exploring the Generalized epsilon-expansion for Self-Avoiding Tethered Manifolds,”
Phys. Rev. A 41, 1751-1755 (1990).

T. Hwa and M. Kardar,
“Dissipative Transport in Open Systems: An Investigation of Self-Organized Criticality,”
Phys. Rev. Lett. 62, 1813-1816 (1989).

E. Medina, T. Hwa, M. Kardar and Y.-C. Zhang,
“Renormalization-Group Studies of the Burgers’ Equation with Correlated Noise,”
Phys. Rev. A 39 , 3053 (1989).

T. Hwa and M. Kardar,
“Evolution of Surface Patterns on Swelling Gels,”
Phys. Rev. Lett. 61, 106-109 (1988).

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