Chalk Talks

2015 May 21

Chalk Talk - Alán Aspuru-Guzik, Professor of Chemistry and Chemical Biology

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St

Abstract - My group members and myself are interested in the energy cycles of prebiotic molecular networks and metabolism. To be able to explore such networks, we have developed methods that combine heuristic reaction rules with quantum chemical calculations to be able to explore quickly the highly-dimensional potential energy surfaces associated with these reactions. We have explored the formose reaction and compared its network properties to those of metabolic networks. We also have explored the non-enzymatic reverse tricarboxilic acid cycle to determine its uniqueness amongst other...

Read more about Chalk Talk - Alán Aspuru-Guzik, Professor of Chemistry and Chemical Biology
2015 Mar 05

Chalk Talk -Mimicking the properties of Life with a Generic Stochastic Reaction-Diffusion System, Alberto Munuzuri (EPS - Perez-Mercader Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Life and living systems (LS) constitute the most complex class of natural phenomena that we know on Earth and, at least for now, in the Universe. Their functioning involves thousands of biochemical reactions and processes, all working at many different temporal and spatial scales. When it comes to understand Life and its properties, the traditional approach is to start from details and work from there to a full understanding of the complete system, i.e. a bottom-up process. In this talk we will discuss a completely different, but complementary, (top-down) approach. Starting from basic...

Read more about Chalk Talk -Mimicking the properties of Life with a Generic Stochastic Reaction-Diffusion System, Alberto Munuzuri (EPS - Perez-Mercader Group)
2015 Feb 05

Chalk Talk -Study on Bacterial Protein Synthesis System toward the Incorporation of D-Amino Acid - Po-Yi Huang (HMS- Church Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract:Life is anti-entropic and highly organized phenomenon with two characteristics reinforcing each other: homochirality and the stereospecific catalysis of chemical reactions. The exclusive presence of L-amino acids and R-sugars in living world well depict this. Hypothetically, the amino acids and sugars of reverse chirality could form a parallel kingdom which is highly orthogonal to the present world. The components from this mirror kingdom, such as protein or nucleic acid, will be much more resistant to the defensive mechanism of present living system, which could be of great value...

Read more about Chalk Talk -Study on Bacterial Protein Synthesis System toward the Incorporation of D-Amino Acid - Po-Yi Huang (HMS- Church Group)
2015 May 07

Chalk Talk - "The Origin of the Moon and the Current Isotopic Crisis." Kun Wang (EPS - Jacobsen Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Numerical simulations have been used to support the hypothesis that the Earth-Moon system is the product of an ancient catastrophic Giant Impact event. The original simulations suggested that the Moon was made mostly from the impactor material with only minor contributions from the Earth. In contrast, isotopic studies have demonstrated that the Earth and Moon are remarkably similar in their isotopic compositions for many elements (e.g., O, Ti, Cr and W isotopic anomalies and Mg and Si stable isotopes). This similarity between the Earth and Moon is unique in our Solar System when...

Read more about Chalk Talk - "The Origin of the Moon and the Current Isotopic Crisis." Kun Wang (EPS - Jacobsen Group)
2015 Apr 02

Chalk Talk - Natural nuclear reactors as a case study for coupled thermodynamic feedback and organic synthesis in geological systems- Zachary Adam (EPS - Knoll Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract:  Energy dissipation processes in abiotic systems is typically unidirectional, ranging from the gentle rain of sunshine to the explosive release of an impactor. Though these and other dissipation processes have served as invaluable prebiotic synthesis scenarios, the thermodynamics of such systems are inherently problematic for origins of life studies. Mass transport, thermal and chemical gradients converge and interact on short systemic scales to freeze reactants into organic matter, but work and information flow rarely result in stable circulatory patterns that link chemical...

Read more about Chalk Talk - Natural nuclear reactors as a case study for coupled thermodynamic feedback and organic synthesis in geological systems- Zachary Adam (EPS - Knoll Group)
2014 Nov 06

Chalk Talk - Dmitry Zubarev -CCB - Reconstruction of Prebiotic Reaction Networks

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street
Abstract: The central ambition of theoretical chemistry is to describe chemistry in its diversity solely as a solution to Schrodinger Equation. The difficulty of this strategy is that it has to capture development of molecular systems at multiple spatiotemporal scales which is prohibitively 
expensive. Prebiological chemistry is the most challenging in this sense because the target phenomenon - the emergence of life - cannot be meaningfully represented as a collection of independent events at the level of organic reactions,...
Read more about Chalk Talk - Dmitry Zubarev -CCB - Reconstruction of Prebiotic Reaction Networks
2014 Dec 04

Chalk Talk - Noam Prywes & Ben Adlam - On the Exploration of Evolutionary Landscapes

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

The evolutionary space of a single enzyme is far too large to explore systematically.  Despite this, there has been much success in the field of in vitro evolution, both from enzymes with starting activity and from random sequence.  What can we say about the structure of evolutionary space based on these findings?  What can we say about optimal methods for the discovery and improvement of enzymes?  Drawing on recent experimental and theoretical work we will go over several ways by which this problem has been approached in the past and will explore questions of how to...

Read more about Chalk Talk - Noam Prywes & Ben Adlam - On the Exploration of Evolutionary Landscapes
2014 Oct 02

Origins Chalk Talk - William Shih, Ph.D. (Wyss Institute-HMS) - 3D Digital Nanofabrication and Scaffolding of Lipids via DNA Self-Assembly

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract: A key challenge for nanotechnology is the programmable self-assembly of complex nanostructures. Our laboratory pioneered a versatile general solution: custom three-dimensional shapes, the size of small viruses, that can be conceived as stacked sheets woven from parallel DNA double helices. Current work is focused on achieving greater complexity via hierarchical self-assembly, and exploring site-specific chemical functionalization and programmable actuation. We also have been studying capture of lipid bilayers on the surface of DNA-origami nanostructures. One of...

Read more about Origins Chalk Talk - William Shih, Ph.D. (Wyss Institute-HMS) - 3D Digital Nanofabrication and Scaffolding of Lipids via DNA Self-Assembly
2014 May 01

Chalk Talk - "Activity based protein profiling and the puzzle about the origin of life" (Evelyn Zeiler - Harvard)

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Evelyn Zeiler
Origins Postdoctoral Fellow - Dept. of Earth & Planetary Sciences (Pearson Lab)

One of the fundamental processes of the origin of life is the need to separate biochemical reactions from the environment to build the first cells. Under the extreme conditions of early Earth, the need for membrane stability would have been paramount. The domain of Archaea exists in a broad range of habitats on Earth, and many extremophilic species are near the root of the phylogenetic tree of life. Their capabilities to survive a wide range of temperature, pH, pressure, and...

Read more about Chalk Talk - "Activity based protein profiling and the puzzle about the origin of life" (Evelyn Zeiler - Harvard)
2014 Apr 03

Chalk Talk - "Towards controlled formation of amphiphilic molecules: insights from inorganic chemistry" (Jan Szymanski - Harvard)

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Jan Szymanski
Postdoctoral Fellow - Dept. of Earth & Planetary Sciences (Perez-Mercader Group)

For each of the three most important characteristics of extant living systems (membrane boundary, metabolism, information-carrying polymers), there exists an origins-of-life school of thought positing that one of them preceded the others along the path from non-life to life. The interconnectedness makes, however, exploring any of the three in the absence of the rest extremely difficult. In this talk, I am going to present some results regarding looking instead at a pair of...

Read more about Chalk Talk - "Towards controlled formation of amphiphilic molecules: insights from inorganic chemistry" (Jan Szymanski - Harvard)
2014 Mar 06

Chalk Talk - "The Quest for Small Planets Orbiting Small Stars" (Courtney Dressing - Harvard)

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Courtney Dressing
Graduate Student - Dept. of Astronomy

Contrary to popular perception, the Sun is not a typical star. Roughly 75% of stars in the galaxy are actually smaller and cooler stars known as red dwarfs. Because most stars are red dwarfs, quantifying the fraction of red dwarfs that host planets and exploring properties of those planets is critical for advancing our knowledge of the overall population of planets in the galaxy. I will explain how the exquisite data obtained by the NASA Kepler mission has allowed us to estimate the fraction of red...

Read more about Chalk Talk - "The Quest for Small Planets Orbiting Small Stars" (Courtney Dressing - Harvard)
2014 Feb 06

Chalk Talk - "Solar System history from the asteroid belt's perspective" (Francesca DeMeo - Harvard)

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Francesca DeMeo
Postdoctoral Fellow - Harvard College Observatory

Asteroids and other small bodies are markers, like tiny beacons, relaying information about the initial temperature and composition conditions of our Solar System revealed by their surface compositions, as well as the Solar System’s evolution fossilized in the scattering record of these bodies. They are also the building blocks of the terrestrial planets, supplying both organic matter and water, essential for life as we currently understand it. In this talk I will begin by providing context for the...

Read more about Chalk Talk - "Solar System history from the asteroid belt's perspective" (Francesca DeMeo - Harvard)
2013 Dec 05

Chalk Talk - "A Song of Ice and Fire - Evolution of small icy bodies and their planetary context"

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Gal Sarid
Postdoctoral Fellow - Dept. of Earth & Planetary Sciences (Stewart Lab)

The nature of icy-rocky minor bodies is one of the central themes in planetary science. Investigation of primitive bodies addresses questions about the initial stages, conditions, and processes during solar system formation, and the sources of organic and volatile material to the planets. With the on-going development of observing techniques and instruments, there are several potential analogs to our own diverse population of minor bodies littering other circum-stellar systems. These serve as...

Read more about Chalk Talk - "A Song of Ice and Fire - Evolution of small icy bodies and their planetary context"
2013 Nov 14

Chalk Talk - "Oligomer assisted non-enzymatic RNA polymerization"

9:00am to 10:00am

Location: 

Naito Laboratory, Room 205 12 Oxford Street

Noam Prywes
Graduate Student - Dept. of Chemistry & Chemical Biology (Szostak Lab)

A central tenet of the RNA world is that RNA polymerases could replicate themselves.  Over the last 20 years, RNA-dependent RNA polymerases have been evolved that can copy RNA sequences longer than themselves.  The development of these polymerases required many rounds of selection and amplification.  Since amplification would have required a polymerase there appears to be a paradox.

Non-enzymatic polymerization has been proposed as a solution to this paradox. ...

Read more about Chalk Talk - "Oligomer assisted non-enzymatic RNA polymerization"

Pages