About

I was born in Vietnam but came to the U.S. during high school through a cultural exchange program. Since then I have graduated from Massachusetts Institute of Technology with a B.Sc. Degree and Princeton University with a Ph.D. Degree (thesis “Swarm Intelligence in Natural and Synthetic Lives“).

My main interest is exploring unconventional ideas (such as the emergence of intelligence at microbial level and the robo-biology of artificial lifeforms), but for credibility I also have worked on many conventional scientific topics (such as emergent swarm behavior in active matter, information theory, evolutionary cancer biology, cell morphology & motility, protein-folding and opto-thermo-electrical transport in condensed matter physics). I see myself as a physicist, but my research journey has also made me a biologist and a roboticist.

I was a postdoc in the Department of Molecular, Cellular and Developmental Biology at Yale University. I am now a postdoc in the Department of Chemical and Biomolecular Engineering at Johns Hopkins University, and also affiliated with Johns Hopkins Medical Institute. My life is blessed with an amazing family, good friends, and great teachers.

Here is my CV.

Notable Media Coverages

Media coverage of our work on emergent bacterial swarm intelligence as they navigate through non-trivial topology mazes and invade lung-like fractal spaces: WIRED.

Media coverage of our work on emergent states of synthetic life on a programable interactive landscape. We call the robot bootstrapped locomotion due to spontaneous symmetry-breaking “field-drive,” similar to “warp-drive” in general relativity, as it is based on the back-reaction of “resource-space” warping around a robot: APS Physics, Epsiloon.

Media coverage of our work on how analog simulations can help optimizing cancer treatment. The robobiological experiments bring new insights into biological evolution and suggest a way to improve chemotherapy. Instead of periodic doses of a single drug, stochastic doses of multiple drugs could be more effective: Physics Today. This is a new and exciting field in biology: Let the robotic games begin!

Media coverage of our work on developing a tool for estimating the local entropy production rate based on time-reversal asymmetry, linking the local dynamics to global pattern formation and creating the visualization & quantification of how information is transferred in living systems: APS Physics. A figure from this paper is the cover picture of Physical Review Letter Volume 129 Issue 22.

Notable Professional Activities

I’m a referee for Proceedings of the National Academy of Sciences and Biophysical Journal. In the summer, if time permits I teach enlisted veterans S.T.E.M. and lab skills for the Warrior-Scholar Project.

I was a Graduate Teaching Fellow at McGraw Center, Princeton University. During my undergrad, I developed some of the notes for high-energy physics courses at M.I.T. OCW and EdX such as 8.851 Effective Field Theory and 8.821 String Theory and Holographic Duality.

Notable Research Findings

Biophysics:

Phan, T. V., Morris, R., Black, M. E., Do, T. K., Lin, K. C., Nagy, K., Sturm, J. C., Bos, J., & Austin, R. H. (2020). “Bacterial Route Finding and Collective Escape in Mazes and Fractals.” Physical Review X, 10(3), 031017.

Natural complex topologies form challenging existential puzzles for bacteria. Billions of years of evolution have shaped the response of bacteria to these puzzles, whose solutions can be found in how bacteria such as the common E. coli respond collectively and individually to challenges. We pose challenges to bacteria in the forms of mazes and fractal spaces, showing the unexpected and clever (if we can say that word about bacteria) way in which they are able to efficiently explore nontrivial mazes in times much shorter than a no-memory walk would predict, and can collectively escape from a fractal topology.

Guo, B.*, Ro, S.*, Shih, A., Phan, T. V., Austin, R. H., Martiniani, S., Levine, D., & Chaikin, P. M. (2022). “Model-free measurement of local entropy production and extractable work in active matter.” Phys. Rev. Lett. 129, 220601. [*co-first authors].

Time-reversal symmetry breaking is a universal feature of active and living systems. Here we introduce a model-free local measure of entropy production as a metric of time-irreversibility and a numerical protocol to estimate it, then establish a connection to the extractability of work in a given region of the system. We validate our approach in theory, simulation, and experiments by considering systems of active Brownian particles and E.coli bacteria.

Robophysics:

Wang, G.*, Phan, T. V.*, Li, S., Wombacher, M., Qu, J., Peng, Y., Chen, G., Goldman, D. I., Levin, S., Austin, R. H., & Liu, L. (2021). “Emergent Field-Driven Robot Swarm States.” Phys. Rev. Lett. 126, 108002. [*co-first authors].

A swarm of small robots can imitate deer or bacteria searching for food. We release these electronic foragers on an LED screen whose light output was adjusted to mimic the amount of a consumable resource—such as grass for deer. Once the robots “ate” the resource in one place, they can sense that they are in a depleted region and will move in the direction of more food; we call this emergent symmetry-breaking motion “field drive” (which is analogous to the general relativistic “warp drive,” as it is based on the warping of the “resource space” around a robot). This programmed behavior led to collective patterns that resembled phases of matter including liquid, crystal, and glass.

Wang, G.*, Phan, T. V.*, Li, S., Wang, J., Peng, Y., Chen, G., Goldman, D. I., Levin, S. A., Pienta, K., Amend, S., Austin, R. H., & Liu, L. (2022). “Robots as Models of Evolving Systems.” Proceedings of the National Academy of Sciences, 119(12), e2120019119. [*co-first authors].

Perhaps someday synthetic life may ultimately co-exist with biological life, and it may learn from biology how to survive. To study a form of robobiology with embedded evolution dynamics which have been so successful for the dominance of biological life, we have developed in emulation of natural systems analog/digital interactive motile robots which move over multiple dynamic resource landscapes that they themselves change. We discover an interesting sector of evolution, in which the survivability of fast-mutating robots can be strongly suppressed under stochastic changes when they respond to resources that they neither consumed nor needed. In biology, the ability of a gene to influence two or more unrelated physical traits is known as pleiotropy, which has been implicated in cancer cells’ resistance to chemotherapy. This finding suggests a way to improve chemotherapy: instead of periodic doses of a single drug, stochastic doses of multiple drugs could be more effective.

Other Research

Biophysics:

Phan, T. V.*, Li, S.*, Ferreris, D., Morris, R., Bos, J. A., Guo, B., Martiniani, S., Chaikin, P. M., Kevrikidis, Y. G., & Austin, R. H. (2023). “Bacterial Collective Entropy Generation and Population Inversion Near a Hydrodynamic Black Hole.” (in preparation). [*co-first authors]

Nagy, K., Valappil, S. K., Phan, T. V., Dér, L., Morris, R., Bos, J. A., Winslow, S., Galajda, P., Rákhely, G., & Austin, R. H. (2023). “Transient Bacterial Clusters Drive de novo T4r Phage Resistance in Complex E. coli Ecologies.” (in preparation).

Zhao, Y., Kimberly Shen, K., Hosny, N., Qu, J., Amend, S., Hammarlund, E., Brown, J., Pienta, K., Phan, T. V., Butler, G. , Austin, R. H. (2023). “Metastatic Prostate Cancer Cell Movement, Metabolism and Survival In Self-Generated Hypoxia.” (in preparation).

Phan, T. V.*, Mattingly, H. H.*, Vo, L., Marvin, J. S., Looger, L.L., & Emonet, T. (2023). "Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model." bioRxiv preprint. (in review, Proceedings of the National Academy of Sciences). [*co-first authors].

During collective cellular processes, cells often dynamically shape and respond to their chemical environments. Our understanding of these processes is limited by the ability to measure these chemical profiles in real time. Here we used a biocompatible fluorescent protein sensor to directly observe attractant gradients created and chased by collectively-migrating bacteria. Doing so uncovered limitations of the standard chemotaxis model at high cell densities and allowed us to establish an improved model. Our work demonstrates the potential for fluorescent protein sensors to measure the spatiotemporal dynamics of chemical environments in cellular communities.

Sun, Y., Liao, D., Torga, G., Phan, T. V., Brown, J., Hammarlund, E., Amend, S., Pienta, K. J., & Austin, R. H. (2023). "The physics of cancer recurrence and metastasis." (in review, Rev. Mod. Phys.).

We have tried to explore, from a physics perspective, why it is that metastatic cancer remains such an unsolved problem. We have tried to emphasize that the field of physics has much to offer in methodology to crack the nut of lethal cancer. We would like to think that this review could serve as a call to arms for the physics community. We urge you to seek out the cancer biologists and oncologists around you, and ask ”How can I help?”

Phan, T. V.*, Wang, G.*, Do, T. K., Kevrekidis, I. G., Liu, L., & Austin, R. H. (2021). “It Doesn’t Always Pay to be Fit: Success Landscapes.” Journal of Biological Physics, 47(4), 387-400. [*co-first authors].

We discuss a form of landscape in evolutionary biology which takes into account (1) initial growth rates, (2) mutation rates, (3) resource consumption by organisms, and (4) cyclic changes in the resources with time. Although our analysis is purely theoretical, we believe the results have possibly strong connections to how we might treat diseases such as cancer in the future with a deeper understanding of the interplay between resource degradation, mutation, and uncontrolled cell growth.

Khuri, R. R., Phan, T. V., & Austin, R. H. (2021). “Protein Dynamics Implications of the Low and High Temperature Denaturation of Myoglobin.” Phys. Rev. E 104, 034414.

We derive an exact thermodynamic expression for cold denaturation and give a better approximation than exists in the literature for predicting cold denaturation temperatures in the two-state model of protein folding. We discuss the “dark-side” implications of this work for previous temperature-dependent protein dynamics experiments.

Phan, T. V., Morris, R. J., Lam, H. T., Hulamm, P., Black, M. E., Bos, J., & Austin, R. H. (2018). “Emergence of Escherichia coli critically buckled motile helices under stress.” Proceedings of the National Academy of Sciences, 115(51), 12979-12984.

We discover an emergent mechanism by which E.coli can escape high-stress regions, such as near-lethal concentrations of antibiotics, by forming long motile helical filaments that are poized at the critical shear buckling point: 2π twist rotations independent of the length of the filament.

Morris, R. J., Phan, T. V., Black, M., Lin, K. C., Kevrekidis, I. G., Bos, J. A., & Austin, R. H. (2017). “Bacterial population solitary waves can defeat rings of funnels.” New Journal of Physics, 19(3), 035002.

We show that the bacterial population is able to defeat the physical constraints of the funnels by launching back-propagating collective waves which rapidly circle the device and radiate inwards against the pumping action of the funnel. This poses a puzzle: what can it mean, or, rather, how does this increase the fitness of the bacteria in our device? We think it has to do with collective intelligence, in which we has presented some evidences for in Physical Review X, 10(3) (2020), 031017.

Robophysics:

Phan, T. V.*, Wang, G.*, Liu, L., & Austin, R. H. (2021). “Bootstrapped Motion of an Agent on an Adaptive Resource Landscape.” Symmetry, 13, 225. [*co-first authors].

We theoretically show that isolated agents that locally and symmetrically consume resources and sense positive resource gradients can generate constant motion via bootstrapped resource gradients in the absence of any externally imposed gradients, and we show a realization of this motion using robots. This self-generated agent motion can be coupled with neighboring agents to act as a spontaneously broken symmetry seed for emergent collective dynamics, which has been verified in Phys. Rev. Lett. 126 (2021), 108002.

Condensed Matter Physics:

Li, S.K.*, Phan, T.V.*, Wang, G., Khuri, R.R., Austin, R.H., & Liu, L. (2023). “Emergence of Broken Symmetry Via Odd Viscosity in Inertial Spinner Swarms.” arXiv preprint arXiv:2303.08223. (in review, Communications Physics). [*co-first authors].

We have created an inertial motile chiral active matter consisting of two opposite-handedness species of spinners floating on an air-table. The spinners can act as their own anti-particles, annihilating their net spins to generate large amounts of translational orbital angular momentum. In this form of matter, the rotational energy can become highly localized, with the minority species pumped preferentially to high spin. At high density, where tertiary and higher number collisions become dominant, the time course of mixing entropy in the system exhibits oscillatory recurrence, indicating an emergent memory capability. If the spinners are geometrically confined, different spontaneous topological arrangements can lock the spinners into distinct frustrated spinning states, which gives a gearbox foundation for scale-free fractal machines.

Borgnia, D. S., Phan, T. V., & Levitov, L. S. (2015). “Quasi-Relativistic Doppler Effect and Non-Reciprocal Plasmons in Graphene.” arXiv preprint arXiv:1512.09044.

We made a theoretical prediction that plasmonic propagation can experience the Doppler effect and also get dragged by an electrical DC current, analogous to the Fizeau effect in which light can get dragged by moving media. This has been verified experimentally in Nature 594.7864 (2021): 513-516 and Nature 594.7864 (2021): 517-521.

Phan, T. V., Song, J. C., & Levitov, L. S. (2013). “Ballistic heat transfer and energy waves in an electron system.” arXiv preprint arXiv:1306.4972.

We made a theoretical prediction that a ballistic energy transfer mode, with heat propagation governed by a wave equation rather than a diffusion equation, can be realized for a thermal electron-hole plasma in graphene. This has been verified experimentally in Nature 557.7706 (2018): 530-533 and Nature 614.7949 (2023): 688-693.

Applied Math:

Do, T. K.*, & Phan, T. V.* (2022). “Equal Radiation Frequencies from Different Transitions in the Non-Relativistic Quantum Mechanical Hydrogen Atom.” Quantum Reports, 4(3), 272-276. [*co-first authors]

Is it possible that two different energy-level transitions in the non-relativistic quantum mechanical model of the hydrogen atom give the same photon radiation frequency? This was a famous puzzle that was quite popular with physics grad students, and was "unsolved", until we provided a general solution and generalized it to families of equifrequency transitions.

Phan, T. V., & Doan, A. (2021). “A Curious Use of Extra Dimension in Classical Mechanics: Geometrization of Potential.” Journal for Geometry and Graphics, 25(2), 265-270.

We show how a special family of potentials can be geometrized by adding two extra dimensions, one spatial and one temporal. This paper comes from combining our final projects for a class during our undergrad.

Education & Miscellaneous:

The following technical reports are side-projects with Vietnamese high school students in the xPhO Physics Club. Most of these are solutions to curious questions in classical physics, but some are actually new scientific discoveries. I find it very joyful and extremely rewarding to guide young people doing research.

Nguyen, M. D. N.*, Pham, P. H.*, Ngo, K. V., Do, V. H., Li, S., & Phan, T. V. (2023). “Remark on the Entropy Production of Adaptive Run-and-Tumble Chemotaxis.” Physica A: Statistical Mechanics and its Applications: 129452. [*co-first authors].

We present the general framework for calculating the entropy production rate created by such population of agents from the first principle, using the minimal model of bacterial adaptive chemotaxis, as they execute the most basic collective action -- the mass transport. This provides a measure for estimating the maximum extractable power from active matter systems that can be controlled via external chemical fields.

Ao, V. D., Tran, D. V., Pham, K. T., Nguyen, D. M., Tran, H. D., Do, T. K., Do, V. H., & Phan, T. V. (2023). “A Schrödinger Equation for Evolutionary Dynamics.” Quantum Reports, 5(4): 659-682.

We establish an analogy between the Fokker–Planck and Schrödinger equations, showing that the stationary population distribution corresponds exactly to the ground-state wavefunction. This equivalence enables us to use quantum mechanics tools for reasonable quantitative assessments and explorations of fundamental biological inquiries. We show that, even in an unchanging environment, a sharp mutational burst resulting from stress can always be advantageous, while a gradual increase only enhances population size when the number of relevant evolving traits is limited.

Pham, K. T.*, Nguyen, D. M.*, Tran, D. V., Ao, V. D., Tran, H. D., Do, T. K., & Phan, T. V. (2023). “Stress-Induced Mutagenesis Can Further Boost Population Success in Static Ecology.” arXiv preprint arXiv: 2303.09084. (in review, Bulletin of Mathematical Biology). [*co-first authors].

We have developed a mathematical model that captures stress-induced mutagenesis, a fundamental aspect of pathogenic and neoplastic evolutionary dynamics, on the fitness landscape with multiple relevant genetic traits as a high-dimensional Euclidean space. In this framework, stress-induced mutagenesis manifests as a heterogeneous diffusion process. We show how increasing mutations, and thus reducing exploitation, in a static ecology with fixed carrying capacity and maximum growth rates, can paradoxically boost population size. Remarkably, this unexpected biophysical phenomenon applies universally to any number of traits.

Tran, C. Q., Nguyen, H. N., Nguyen, A. T. & Phan, T. V. (2022). "Edge of Infinity: The Clash between Edge Effect and Infinity Assumption for the Distribution of Charge on a Conducting Plate." arXiv preprint arXiv:2210.13665 (in review, American Journal of Physics).

We revisit a common introductory physics problem involving induced charge distribution on an uncharged conducting plate when a uniformly charged dielectric plate is placed parallel to it. We show that, regardless of plate size, the edge effect significantly impacts the charge distribution in the central region, destroying the infinity assumption completely.

Nguyen, H. N., Tran, C. Q., Nguyen, A. T. & Phan, T. V. (2022). "The Effect of Charge Discretization on the Electrical Field inside a Conductor." arXiv preprint arXiv:2208.00350 (accepted by The Physics Teacher).

We illustrate the effect of charge discretization on a fundamental emergent law of electrostatics. We show that the electrical field inside a conductor is non-vanishing, concentrated near the surface at a shallow depth which depends on the finite number of charged-particles.

Nguyen, L. T., Do, T. K., Nguyen, D. V. & Phan, T. V. (2021). “On the Electrostatic Interaction between Point Charges due to Dielectrical Shielding.” Progress In Electromagnetics Research Letters, Vol. 107, 111-118.

Nguyen, L. K., Tran, T. X., Nguyen, Q. M., Tran, C. D., Cai, T. H., & Phan, T. V. (2021). “Elementary Methods for Infinite Resistive Networks with Complex Topologies.” arXiv preprint arXiv: 2105.03690.

Nguyen, Q. M., Nguyen, L. K., Tran, T. X., Tran, C. D., Cai, T. H., & Phan, T. V. (2020). “Infinite AC ladder with a twist.” arXiv preprint arXiv: 2010.05645.