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The Bridge: 50th Anniversary Issue
January 7, 2021 Volume 50 Issue S
This special issue celebrates the 50th year of publication of the NAE’s flagship quarterly with 50 essays looking forward to the next 50 years of innovation in engineering. How will engineering contribute in areas as diverse as space travel, fashion, lasers, solar energy, peace, vaccine development, and equity? The diverse authors and topics give readers much to think about! We are posting selected articles each week to give readers time to savor the array of thoughtful and thought-provoking essays in this very special issue. Check the website every Monday!

Consciousness and Convergence: Physics of Life at the Nanoscale

Monday, January 18, 2021

Author: Anita Goel

The consciousness with which science is pursued plays a critical role in shaping scientific worldviews, the fundamental questions asked, and the technologies created and their ultimate impacts on society.

My childhood exposure, while growing up in the rural landscapes of -Mississippi, to meditation and Eastern philosophy instilled in me a worldview that it should be possible to understand the far reaches of the universe and living systems with one integrated, holistic conceptual framework that is self-consistent and mathematically rigorous. As a physicist and physician-scientist, I founded Nanobiosym as a research institute and idea lab to consciously converge physics and biology at the nanoscale in an emerging field we call nanobiophysics.

From Reductionism to Convergence

Over the past 500 or so years, modern science has made great strides, albeit in a predominantly reductionist paradigm, whereby complex systems were assumed to be fully understood as the simple sum of their parts.

Twentieth century physics and biology largely developed as separate disciplines. Physics was formulated in the context of nonliving matter. Its mathematical language dealt primarily with closed systems that operated at or near equilibrium; any interaction with the environment was considered, at best, a small perturbation to these closed systems. In contrast, living systems are fundamentally open and continuously exchange matter, energy, and information with their environment.

Despite the advent of thermodynamics, statistical mechanics, and quantum mechanics, physics had not yet developed adequate mathematical and conceptual tools to predict the behavior of nonequilibrium systems that are strongly coupled to their environment. Nanotechnology provides the practical tools and conceptual platform to bring the seemingly divergent worlds of physics and biomedicine under a common roof.

Using DNA Nanomachines to Probe the Interplay of Matter, Energy, and Information

Biological information is replicated, transcribed, or other-wise processed by nanoscale biomotors or molecular engines that convert chemical energy stored in nucleotides into mechanical work. The dynamics of a molecular motor depend not only on the DNA sequence it reads but also on the environment in which it operates—the environment influences the way cells process the information encoded in DNA (Goel 2008, 2010).

Goel figure 1.gif

FIGURE 1 Experimental data for tension dependence of net DNA replication rate can be explained by a network model of a nanomachine. A single DNA molecule is stretched (tension f, in piconewtons, pN) between two beads (top). In each forward step, the enzyme (DNA polymerase, DNAp) motor incorporates one nucleotide (dNTP) into the DNA and releases one molecule of pyrophosphate (PPi) into the surrounding solution. As the enzyme motor visits the sequence of states 3 ® 4 ® 5 ® 6 ® 7 ® 3¢, it completes one polymerase cycle (red); a switch of 3 ® 2 enables the sequence 2 ® 2¢, completing one exonuclease cycle (green). Distinct cycles for polymerase (red) and exonuclease (green) pathways are linked by a cycle (black) involving binding or unbinding of the motor to the DNA. This biological network corresponds to the internal state transitions that occur in this DNAp-DNA complex functioning like an algorithmic state machine undergoing internal transitions as the DNAp motor enzyme trans-locates along a molecule of DNA. Jpoly denotes the net forward or -polymerization rate and Jexo denotes the net backward or exonuclease rate. The experimental data from single molecule experiments are denoted via the green triangles and diamonds and indicate the net replication rate at a given force or tension on the stretched molecule of DNA. The red trendline describes how our network model can reconcile our simple open biological network models with actual single molecule experimental data. Arrows indicate how the network dynamics are coupled to various environmental parameters where transition rates between internal nodes are proportional to external environmental parameters such as ambient concentrations of enzyme, nucleotide, or pyrophosphate or tension f used to stretch the DNA. dNMP = -deoxyribonucleoside monophosphate; Jexo = flux or net rate of exonuclease activity; Jpoly = flux or net rate of polymerization. Adapted from Goel and Vogel (2008) and Goel et al. (2002).

We have developed a self-consistent physics framework to quantitatively describe how environmental cues (e.g., temperature, ambient concentrations of nucleotides and other biochemical agents, the amount of mechanical tension or torsional stress on the DNA) directly couple to the dynamics of the nanomotor (figure 1). The resulting information will yield a better understanding of the context-dependent function of these DNA-reading nanomachines (Goel 2008, 2010; Goel and Herschbach 2003), with potential impacts and applications described in the next section.

Our framework (Goel 2002) suggests that the information or number of bits stored in a DNA motor system is much larger than conventionally assumed (Goel 2008), that the DNA, the replicating motor, and its environment constitute a dynamic and complex network with dramatically higher information storage and processing capabilities. The information storage density results, in part, from the motor itself having several internal microscopic states, each representing a decision point in the nanomotor’s trajectory.

As the nanomachine moves along DNA it must process information and integrate environmental inputs from multiple levels to determine exactly how it reads the DNA. Learning how to control and manipulate the performance of nanomotors externally is a critical hurdle in harnessing them for ex vivo applications. By identifying or engineering appropriate external “knobs” in the motor or its environment, its nanoscale movement can be tightly regulated, switched on and off, or otherwise manipulated on demand. At Nanobiosym we are harnessing the nanomachines for a variety of practical applications, from portable diagnostics to molecular manufacturing of biopolymers, biological classical and quantum computation, nanoscale information storage in biomaterials, and ultra-efficient energy transduction schemes.

Rewriting the Rules of Medical Diagnosis with Nanobiophysics

Current best-in-class molecular diagnostics systems are based on a 35-year-old method that requires large bulky machines and extensive overhead infrastructure, complex sample transport logistics, highly trained personnel, large volumes of expensive reagents, and centralized lab facilities. This system does not lend itself to real-time decentralized precision testing for hundreds of millions of people, as is required in the covid-19 pandemic.

To decentralize these mainframe machines outside of a lab or hospital setting will involve overcoming critical engineering barriers to achieve accuracy, precision, speed, smaller sample sizes, and user-friendliness. My research lab has demonstrated the ability to control molecular machines and more generally molecular reactions at the nanoscale, enabling faster, smaller, IoT--connected, precision-engineered diagnostic devices as well as improved precision and quality control in manufacturing DNA molecules (Goel 2014, 2020).

Nanobiophysics will transform medical diagnosis in practical yet profound ways. Earlier, faster, more accurate detection of infectious diseases can help contain or prevent global pandemics like covid-19, Ebola, avian flu, and SARS, and reduce multidrug-resistant strains of diseases such as HIV, tuberculosis, and malaria.

Today’s gold standard for testing HIV viral load costs $200–300 and can take 2–3 weeks to deliver a result from a centralized lab. In sub-Saharan Africa, the tests can take up to 6 months, given the cost, lack of infrastructure, and difficulty in transporting specimens for molecular level diagnosis. We have developed a platform (the Gene-RADAR) that reduces that time to under an hour, with price points 10–100 times more affordable—all without the need for running water, constant electricity, or highly trained personnel.

The covid-19 pandemic exposed critical gaps in the US public health testing infrastructure. With available testing technologies, less than 5 percent of the population has been tested each month. To reopen the US economy and rehabilitate industries, community-based precision testing is needed for hundreds of millions of people per month. To restore public confidence, the testing technology must be accurate and precise, ideally with no (or very few) false negatives or false positives.

Conclusions

Nanomanufacturing processes, much like macroscopic assembly lines, need procedures that offer precise control over the quality of the product, including the ability to recognize and repair defects. The use of nano-technology to elucidate physical and biological networks can help with this and is just beginning to reveal its potential in other areas.

Viewing a molecular motor as a complex adaptive system that is capable of utilizing information in its environment to evolve or learn may shed light on how information processing and computation can be realized at the molecular level. And by replacing hospitals and centralized labs as the core of healthcare delivery, nanobiotechnology can put the patient and consumer at the center of the healthcare ecosystem.

References

Goel A. 2002. The physics of life. Plenary address, John Wheeler’s Science and Ultimate Reality Symposium, Young Researchers Competition. Princeton University and Institute for Advanced Study. See also Physics Today, May 2002.

Goel A. 2008. Molecular evolution: A role for quantum mechanics in the dynamics of molecular machines that read & write DNA. In: Quantum Aspects of Life, eds Abbott D, Davies PCW, Pati AK. Singapore: World Scientific.

Goel A. 2010. Tuning DNA strings: Precision control of nanomotors. Scientific American, India ed, December.

Goel A. 2014. How nanobiophysics will transform global healthcare. Scientific American Worldview, June.

Goel A. 2020. Precision mobile testing is key to opening the economy safely. Scientific American Worldview, May 27.

Goel A, Herschbach DR. 2003. Controlling the speed and direction of molecular motors that replicate DNA. Fluctuations and Noise in Biological, Biophysical and Biomedical Systems, Proceedings, SPIE 5110:63–68.

Goel A, Vogel V. 2008. Harnessing biological motors to engineer systems for nanoscale transport and assembly. Nature Nanotechnology 3:465–75.

Goel A, Ellenberger T, Frank-Kamenetskii MD, Herschbach D. 2002. Unifying themes in DNA replication: Reconciling single molecule kinetic studies with structural data on DNA polymerases. Journal of Biomolecular Structure and Dynamics 19(4).

Goel A, Astumian RD, Herschbach D. 2003. Tuning and switching a DNA polymerase motor with mechanical tension. Proceedings, National Academy of Sciences 100(17):9699–704.

 

About the Author:Anita Goel is chair, CEO, and scientific director of Nanobiosym R&D Institute and Nanobiosym Diagnostics.