Physical and Quantitative Biology, CHE/PHY 558

Fall 2016 / MWF 10 – 10:50 AM in Laufer Center 101

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving, i.e., the equilibria and transition rates in chemistry, physics and biology. We describe the underpinning components of free energy, the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics and hydrophobic forces - that explain physical and chemical mechanisms in biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for drug discovery; coupled binding explains how biological machines convert energy and transduce signals or regulate gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules.

(Click here to open the course webpage of 2015)

(Click here to open the course webpage of 2014)

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PP = Protein Principles, draft textbook.

ACADEMIC INTEGRITY
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/

ELECTRONIC COMMUNICATION
Email to your University email account is an important way of communicating with you for this course.  For most students the email address is This email address is being protected from spambots. You need JavaScript enabled to view it.¹, and the account can be accessed here: http://www.stonybrook.edu/mycloud.  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: http://it.stonybrook.edu/help/kb/checking-or-changing-your-mail-forwarding-address-in-the-epo. You can set up email forwarding using instructions here: http://it.stonybrook.edu/help/kb/setting-up-mail-forwarding-in-google-mail. If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf. 

Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop¹ period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

DISABILITIES
If you have a physical, psychiatric/emotional, medical or learning disability that may impact on your ability to carry out assigned course work, you should contact the staff in the Disability Support Services office [DSS], 632-6748/9. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the website: http://www.sunysb.edu/ehs/fire/disabilities.shtml.

CRITICAL INCIDENT MANAGEMENT
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the University Police and the Office of University Community Standards any serious disruptive behavior that interrupts teaching, compromises the safety of the learning environment, and/or inhibits students¹ ability to learn. See more here: http://www.stonybrook.edu/sb/behavior.shtml

Physical & Quantitative Biology

CHE 558 / PHY 558

Fall / MWF 10 – 10:50 AM in Laufer Center 101

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand driving forces, i.e., the equilibria and rates in chemistry, physics and biology. We describe the underpinning components, the entropy and energy. We explore the microscopic interactions -- including hydrogen bonding, van der Waals, electrostatics and hydrophobic forces -- that explain physical and chemical mechanisms in biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities are the basis for drug discovery; coupled binding is the basis for how biological machines convert energy and transduce signals; and polymer free energies are the basis for the folding of protein and RNA molecules.

(Click here to open the course page of 2014)

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PP = Protein Principles, draft textbook.

ACADEMIC INTEGRITY
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/

ELECTRONIC COMMUNICATION
Email to your University email account is an important way of communicating with you for this course.  For most students the email address is This email address is being protected from spambots. You need JavaScript enabled to view it.¹, and the account can be accessed here: http://www.stonybrook.edu/mycloud.  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: http://it.stonybrook.edu/help/kb/checking-or-changing-your-mail-forwarding-address-in-the-epo. You can set up email forwarding using instructions here: http://it.stonybrook.edu/help/kb/setting-up-mail-forwarding-in-google-mail. If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf. 

Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop¹ period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

DISABILITIES
If you have a physical, psychiatric/emotional, medical or learning disability that may impact on your ability to carry out assigned course work, you should contact the staff in the Disability Support Services office [DSS], 632-6748/9. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the website: http://www.sunysb.edu/ehs/fire/disabilities.shtml.

CRITICAL INCIDENT MANAGEMENT
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the University Police and the Office of University Community Standards any serious disruptive behavior that interrupts teaching, compromises the safety of the learning environment, and/or inhibits students¹ ability to learn. See more here: http://www.stonybrook.edu/sb/behavior.shtml

Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2023 / MWF 11:00 – 11:53 AM,  in Laufer Center rootm 101.

Recitations: Mon, 12:00 pm – 13:00 pm, in Laufer Center Room 101.

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning free energy: the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics and hydrophobic forces - that explain physical and chemical mechanisms in cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.

Textbook:          Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Extra textbook: Physical Models of Living Systems. W. H. Freeman & Co., 2015

Prior years' course syllabi: 2022 2021, 2020, 2019, 2018, 2017, 2016, 2015, 2014

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs:  Lakshmanji Verma (LV), Chris Helenek (CH).

For videos, please go to Blackboard.

Student Accessibility Support Center Statement
If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632- 6748, or via e-mail at:  This email address is being protected from spambots. You need JavaScript enabled to view it.. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Academic Integrity Statement
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school- specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html

Critical Incident Management
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.

Student Conduct and Community Standards
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn.

Religious Observance
See the policy statement regarding religious holidays at here. Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

 Laufer Center 2015 Spring Retreat

Program

Check-in & Continental Breakfast     8:30 AM – 9:00 AM

Program Opening and Introductions     9:00 AM – 10:00 AM

 9:00        Dr. Ken A. Dill, Opening remarks and Center Overview

 9:45        Drs. Sasha Levy & Gábor Balázsi, Introductions

Oral Session I:     10:00 AM – 12:00 PM

 10:00      Markus Seeliger, Ph.D.

  Department of Pharmacology, Stony Brook University

  Role of protein kinase dynamics for signaling and drug development

 10:30      Jamie Blundell, Ph.D. (advisor:  Sasha F. Levy)

  Postdoctoral Fellow, Laufer Center for Physical & Quantitative Biology

  Quantifying epistasis and the benefit of recombination

 10:45      Kevin Farquhar (advisor:  Gábor Balázsi)

                Genes and Development Ph.D. program, The Graduate School of Biomedical Sciences at Houston

  Phenotypic Impact of Gene Expression Variability in Cancer Biology

 11:00      Adam de Graff, Ph.D. (advisor:  Ken Dill)

                Laufer Jr. Fellow, Laufer Center for Physical & Quantitative Biology

 The Ins and Outs of Aging

 11:15      F. William Studier

  Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory

                Escherichia coli genome evolution

Lunch     12:00 PM – 1:00 PM

Oral Session II:     1:00 PM - 2:45 PM

 1:00        Michael Schatz, Ph.D.

                Cold Spring Harbor Laboratory

  Single cell and single molecule approaches to studying the structure of cancer

  1:30       Justin Gardin (advisor:  Bruce Futcher)

  Molecular Genetics and Microbiology Ph.D. program, Stony Brook University

  Sequence Matters: The Hidden mRNA Code and How it Regulates Protein Levels

 1:45        Jason Wagoner, Ph.D. (advisor:  Ken Dill)

                Laufer Jr. Fellow, Laufer Center for Physical & Quantitative Biology

  Efficiency of molecular motors and cell cycles

 2:00        Daniel Charlebois, Ph.D. (advisor: Gábor Balázsi)

  NSERC Postdoctoral Fellow, Laufer Center for Physical & Quantitative Biology

  Theoretical Investigations on the Development of Nongenetic Drug Resistance

 2:15        Steven Skiena

  Computer Science Department, Stony Brook University

  Optimizing the Design of Coding Sequences

3:00 PM - 4:00 PM

-          Coffee break

-          Poster set-up (ballroom)

-          Free Time (Students & Postdocs)

-          Laufer Center Self-Evaluation (Faculty. Meeting room)

Reception & Poster Session     4:00 PM – 5:30 PM

Poster presenters should be available to answer questions.  

Pizza Dinner & Poster Prizes Awarded     5:30 PM – 6:30 PM

Prizes will be awarded to Grad Students for 1^st and 2^nd place.

Retreat organizers:  Gábor Balázsi and Sasha Levy

 For more information or to request a special accommodation,

contact Nancy Rohring at 631-632-5400 or This email address is being protected from spambots. You need JavaScript enabled to view it.

Check  out our Laufer Center 2015 Spring Retreat T-shirt!