Daniel Aalberts

Daniel P. Aalberts

Kennedy Richardson '71 Professor of Physics

at Williams since 1997

Contact Information

Office: TPL 305
Phone: (413) 597-3520
E-mail: aalberts@williams.edu

Education/Experience

Massachusetts Institute of Technology: S.B. 1989
Massachusetts Institute of Technology: Ph.D. 1994
University of Leiden: Postdoc 1994-1996
Rockefeller University: Fellow 1996-1997, visitor fall 2000

2023-2024 Courses

Phys 151: Seminar in Modern Physics

Courses given previously

Physics 014: The Making of the Atomic Bomb
Physics 018: The Science of Sports
Physics 109: Sound, Light, and Perception
Physics 131: Introduction to Mechanics
Physics 132: Electromagnetism and the Physics of Matter
CSci 134: Introduction to Computer Science
Physics 141: Particles and Waves - Enriched
Physics 151: Seminar in Modern Physics
Physics 201: Electricity and Magnetism
Physics 210: Mathematical Methods for Scientists
Physics 231T: Facts of Life
Phys 302: Statistical Physics
Phys/CSci 315: Computational Biology
Chem/Phys 332: Materials Science
Physics 405T: Electromagnetic Theory
Physics 411T: Classical Mechanics
Phys 451: Condensed Matter Physics

Research interests

Biological polymers, studied with statistical and computational physics techniques.

Optimizing gene expression with mRNA free energy modeling and algorithms

The same protein sequence can be encoded by many different mRNA sequences because of the degeneracy of the genetic code. Variations in mRNA sequence can play an important role in regulating protein expression level; for example, synonymous mutations may alter human susceptibility to diseases. We seek to understand the RNA features controlling gene expression. Analyzing protein expression experiments performed by the Northeast Structural Genomics (NeSG) Consortium, we find that mRNA folding effects dominate in the head region (initial 16 codons), while codon usage dominates in the tail (the remainder). Head and tail have similar overall influence. press release
[Supported by a grant from the National Institutes of Health (GM106372)]

Binding and Splicing mRNA

The famous double helical shape of DNA arises when the bases of the two complementary strands pair. Base-pairing is also the key to allowing special sites of mRNA to be recognized and we have developed a tool BindOligoNet to efficiently calculate Net free energies to optimally Bind Oligo (short pieces) of RNA to long RNA, important for mRNA splicing, siRNA, miRNA, etc. Also, to predict mRNA splice sites, we have used physical chemical models (Finding with Binding) and a novel statistical method (Primary Sequence Ranking).
[Supported by a grant from the National Institutes of Health (GM080690)]

Improving RNA Pseudoknot Models and Algorithms

RNA is more than an intermediary between DNA and proteins, it also modulates gene expression and catalyzes certain reactions. Complementary base pairing condenses RNA into complex, compact shapes. Hairpin or tree-like structures (Fig a) emerge most often, but occasionally the more complicated pseudoknot fold (Fig b) appears.

Pseudoknots are not common, but have amazing functionality when they do appear, catalyzing reactions as enzymes or performing other gene regulation functions. For example, the core of most catalytic RNAs is the interesting pseudoknot fold. Pseudoknots cannot be predicted using traditional RNA folding algorithms. Aalberts and his students have been improving models of pseudoknot structures and have been computing how abundant pseudoknots are.
[Supported by a grant from the National Science Foundation (MCB 0641995)]

The figures depict the molecular backbone and the base pairs.

Physics of Vision:

Rhodopsin, the optically active molecule in our eyes, changes shape when it absorbs a photon. This is the fastest photochemical reaction known --- 200 femtoseconds, less than the time it takes light to cross the width of your hair. Rhodopsin is a highly efficient system with very little noise which is one of the reasons we see when our rod cells are stimulated by only a few photons. I have been developing quantum mechanical models to study how absorption of light creates compact, coherent excitations called solitons and how these may induce the molecular shape change.
[Supported with a Cottrell College Science Award by the Research Corporation]

Selected publications

The four mRNA bases have quite different (un)folding free energies, applications to RNA splicing and translation initiation with BindOligoNet, Julian M. Hess, William K. Jannen, Daniel P. Aalberts J. Mol. Biol 434: 167578 (2022) [doi:10.1016/j.jmb.2022.167578]
Codon influence on protein expression in E. coli correlates with mRNA levels, Gregory Boel, et al, Daniel P. Aalberts and John F. Hunt. Nature 529, 358-363 (2016) [doi:10.1038/nature16509]
Codon Clarity or Conundrum? Daniel P. Aalberts, Gregory Boel, and John F. Hunt. Cell Systems 4, 15-19 (2017) [doi:10.1016/j.cels.2017.01.004 ]
The New Strategies to Overcome Challenges in Protein Production in Bacteria Anna Liponska, Fares Ousalem, Daniel P. Aalberts, John F. Hunt, and Gregory Boel. Microbial Biotechnology 12, 44-47 (2019) [doi:10.1111/1751-7915.13338 ]
Visualizing RNA base pairing probabilities with RNAbow diagrams, Daniel P. Aalberts and William K. Jannen RNA 19, 475-478 (2013) [PDF, preprint] [RNAbows web server]
Free Energy Cost of Stretching mRNA Hairpin Loops Inhibits Small RNA Binding, Yuzhong Meng and Daniel P. Aalberts, Biophysical Journal, 104, 482-487 (2013) [PDF]
Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs, Daniel P. Aalberts, Entropy , 13, 1958-1966 (2011) [PDF]
A Two Length Scale Polymer Theory for RNA Loop Free Energies and Helix Stacking, Daniel P. Aalberts and Nagarajan Nandagopal '09, RNA, 16, 1350-1355 (2010) [PDF]
Quantifying Optimal Accuracy of Local Primary Sequence Bioinformatics Methods, Daniel P. Aalberts, Eric G. Daub '04, and Jesse W. Dill '04, Bioinformatics 21 3347-3351 (2005). [PDF, Primary Sequence Rank web server]
Asymmetry in RNA Pseudoknots: Observation and Theory, Daniel P. Aalberts and Nathan O. Hodas '04, Nucleic Acids Res. 33, 2210-2214 (2005). [PDF]
Efficient Computation of Optimal Oligo-RNA Binding, Nathan O. Hodas '04 and Daniel P. Aalberts, Nucleic Acids Res. 32, 6636-6642 (2004). [PDF, PDFsupp, BINDIGO web server]
Finding with Binding: Thermodynamic Modeling of Donor Splice Site Recognition in pre-mRNA, Jeffrey A. Garland '03 and Daniel P. Aalberts, Phys. Rev. E 69, 041903 (2004). [PDF]
Single-Strand Stacking Free Energy from DNA Beacon Kinetics, Daniel P. Aalberts, John M. Parman '02, and Noel L. Goddard, Biophys. J, 84, 3212 (2003). [PDF]
A Vision for Ultrafast Photoisomerization, Daniel P. Aalberts and Hans F. Stabenau '02, Physica A 389 2981-2986(2010). [PDF]
Quantum Coherent Dynamics of Molecules: A Simple Scenario for Ultrafast Photoisomerization, Daniel P. Aalberts, Lucas du Croo de Jongh, Brian F. Gerke '99, Wim van Saarloos, Phys Rev A 61, 040701 (R) (2000). [PDF]
Towards Understanding the Ultrafast Dynamics of Rhodopsin, Daniel P. Aalberts, Fernando L. J. Vos, and Wim van Saarloos, Pure and Applied Chemistry 69, 2099 (1997).
The Su-Schrieffer-Heeger Model Applied to Chains of Finite Length, Fernando L.J. Vos, Daniel P. Aalberts, and Wim van Saarloos, Phys. Rev. B 53, 14922 (1996).
A Simple Method for Calculating the Speed of Sound in One-Dimensional Tight-Binding Models: Application to the Su-Schrieffer-Heeger Model, Fernando L.J. Vos, Daniel P. Aalberts, and Wim van Saarloos, Phys. Rev. B 53, R5986 (1996).
Electrophoretic Mobility of Asymmetric Reptating Polymers, Daniel P. Aalberts, Phys. Rev. Lett. 75, 4544 (1995). [PDF]
Reptation in a Weak Driving Field, Daniel P. Aalberts and J.M.J. van Leeuwen, Physica A 236, 220 (1997).
Dynamic Symmetry Breaking in a Model of Polymer Reptation, Daniel P. Aalberts and J.M.J. van Leeuwen, Electrophoresis 17, 1003 (1996).

Thesis Students

Brian Gerke '99
[Apker Award for best US undergrad physics research,
MPhil '01 Cambridge Univ (UK),
Ph.D '07 Berkeley, Lawrence Berkeley Lab]
Jonathan Pyle (Swarthmore '99) [J.D., lawyer in Pennsylvania]
Ben Cooper '01 [Ph.D Maryland, now Calico Life Sciences]
Fritz Stabenau '02 [Ph.D '08 UPenn., M.D. '16 Yale]
John Parman '02 [Ph.D '08 Northwestern Econ.,
Prof at William and Mary]
Jeff Garland '03 [Cambridge Univ (UK),
Harvard Law School]
Nathan Hodas '04
[Apker Award for best US undergrad physics research,
Ph.D '11 Caltech, now Pacific Northwest National Lab]
Eric Daub '04 [Ph.D '09 UCSB, Prof at Univ Memphis]
Rob Cooper '06 [Ph.D '12 Princeton]
Alex Zaliznyak '07 [Econ Ph.D student at Stanford]
Sandy Nandagopal '09 [Caltech '17 Ph.D, Harvard]
Becca Sullivan '11 [Teaching Fellow, NYC]
Jeff Meng '11 [Harvard MD-Ph.D program]
Joel Clemmer '12 [Johns Hopkins '19 Ph.D, Sandia Natl Lab]
Julian Hess '13 [Broad Institute]
Mike Flynn '15 [Hutchin Hill Capital; then Caltech PhD]
Bijan Mazaheri '16 [Cambridge Univ (UK), Caltech PhD]
Daniel Wong '17 [Cambridge Univ (UK), Stanford PhD]
Intekhab Hossain '17 [Analysis Group Boston, Harvard Statistics PhD]
Niki Howe '17 [Cambridge Univ (UK), Montreal]
Eliza Matt '18 [InterSystems]
Qiyuan Hu '20 [Amazon, UChicago PhD Program]]
Brendan Hall '21 [UCSF PhD Program]
Theo Tellides '23 [Jane Street]
Saad Waheed '25

Research Students

Ian Eisenman '99 [MS at UCSB,
Environmental physics Ph.D '08 Harvard, UCSD Prof.]
Qiang Sun '00 [Co-founder of www.woya.com]
Rachel Horwitz '03 [US Geological Survey, Ph.D student at Woods Hole/MIT]
Kristina Weyer '03 [Renewable energy M.E. at Colorado St.]
Mike Baiocchi '03 [Statistics Ph.D at UPenn, Stanford Univ Prof.]
Jesse Dill '04 [Biophysics PhD '12 at Berkeley]
Evan Miller '06 [Econ Ph.D program at Univ of Chicago]
Rob Terchunian '06 [U.S. Navy]
Will Parker '08 [Univ. Chicago Medical School]
Jerry He '08 [Cambridge Univ (UK)]
Teng Jian Khoo '09 [Cambridge Univ (UK) PhD 2013]
Scott Olesen '10 [Goldwater Scholar, Cambridge Univ (UK), MIT PhD 2016]
Steven Jackson '10 [Princeton PhD]
Antoniya Aleksandrova '11 [Cambridge Univ (UK) biophysics PhD 2016, NIH postdoc]
Olivia Uhlmann '13 [Teaching at St. Sebastian's School, Needham, MA]
Samantha Petti '15 [Georgia Tech PhD 2020, Harvard postdoc]
Ashwin Narayan '16 [MIT applied math PhD]]
Ian Banta '19 [UCSB PhD]
Tarun Yadav '21 [Applied ML Research]
Maddie Hurwitz '21 [Virginia MD program]
Shayan Moazeni '22
Isaac Wilkins '22 [Cambridge Univ (UK)]
Akira Eisenbeiss '24
Noah Cape '25
Elena Deegan-Krause '26
Terukimi Hayashi '27
Shloke Jani '27

Scientific Programmers

Bill Jannen '09 [Stony Brook Comp Sci PhD 2017, now CS Prof. Williams College]
Mike Flynn '15 [Analyst at Hutchin Hill Capital, now Caltech PhD]

Biography

Curriculum Vitae

Williams Physics